"Was [the] conquest...known to Islamic historians in 1000 AD."
Yes. Alexander the Great was known to Islamic historians and Muslims generally in part because he features prominently in the Qur'an.
I should clarify what I mean by "prominently": readers more familiar with the bible might think that Qur'an is, in the style of the Bible, composed almost as a kind of history, with names and dates and "begats" and all that. It is not. The Qur'an esoterically references a very small number of people, places, and historical events, and exoterically references an even smaller number. (Much of the explanation for these esoteric references, even for supposedly well-known references, is actually only to be found in the Tafsir, the exegesis of the Qur'an, or in the Hadith.)
In the Qur'an, Alexander is referred to obliquely as Dhul Qarnayn. "The Two-Horned One." (NB, this is not a satanic reference. I've read some things that suggest that it might actually be because of coinage that depicts Alexander with horns but I'm not up on where that stands historiographically.)
Now, we don't know that Dhul Qarnayn is Alexander, but he is the very, very clear consensus. Dhul Qarnayn also features in Islamic eschatology because the wall that he built to contain Gog and Magog (either literal monsters or stand-ins for monstrous peoples, for example the Mongol invasions were interpreted by some as Gog and Magog) will be overrun and they will cause apocalyptic damage eventually leading to the actual apocalypse.
In terms of Islamic historians, there is, for example, a chapter on Alexander in al-Tabari. (I'm not sure I can explain succinctly why pointing to Tabari in a sense ought to simply settle this matter. There are probably arguments to be had over whether or not Tabari is the most important classical Islamic historian, but he is certainly the most beloved by historians as colleague. He's a bit like Thucydides in that regard, even in an age when most "historians" weren't especially trustworthy, Islamic studies folks tend to trust Tabari more because he's just kind of a mensch.)
In later literature, Alexander was perhaps more important as a literary figure, although part of my reason for saying that is that I'm not sure if we should really be referring to a lot of the Islamic writers in the Middle Ages as "historians" per se, but also shouldn't dismiss them as such either.
So, for example, Ferdowsi's Shahnameh is a poem. But it's also probably the most significant piece of historical memory in all of Persian literature, let alone Persian literature in circa 1000 AD.
I'll let the Encyclopaedia of Islam do the talking on this because Persian literature is emphatically not a specialty of mine and I think it explains then-contemporary knowledge of Alexander quite well:
For Iranian tradition, he is essentially "the wretched Mar, inspired by the Druj (the spirit of discord)", guilty of the destruction of the good religion, its altars and its books (M. Mol£, Culte, Mythe et cosmologie dans VIran ancien, Paris 1963, 211; cf. Pagliaro, Letteratura persiana, Milan 1950, 38, 96). But in islamised Iran the idea, which was fixed by the commentary of al-Tabari on the Kur'an, XVII, 82 ff. (Tafsir, xvi, 6 ff.) and by the same author's Annales (I, 692-702), of a universal mission made manifest through his conquests, is substituted for this pejorative image.
In the Shahndma, Firdawsi already makes Iskandar an exemplary figure, whom the companionship of Aristotle helps to rise still higher, by the path of wisdom and moderation, in the direction of abstinence and contempt for this world. And Firdawsi laid stress on the defeat of Dara (the Darius of the Greeks) as something desired by "the rotation of the Heavens".
Already, too, for Firdawsi, Alexander bears on his brow the marks of the Kayanids and, thereby, a quality of legitimacy which Nizaml emphasizes by making him, as his predecessor and as al-Tabari had done, a son of Darab and consequently a halfbrother of Dara who is thus able to transmit power over Iran to him, and to see in him the just king, the successor of the Kayanids.
At the time of Nizaml, however, Islam is from then onwards well established in Iran, and it is the prophetic and ecumenical aspect of his destiny that the poet makes evident in his hero. As a learned Iranian poet, Nizaml, who demonstrates his eclecticism in the information he gives (he says, "I have taken from everything just what suited me and I have borrowed from recent histories, Christian, Pahlavi and Jewish . . . and of them I have made a whole"), locates the story of his hero principally in Iran. He makes him the image of the Iranian "knight", peaceloving and moderate, courteous and always ready for any noble action. Like all Nizami's heroes, he conquers the passions of the flesh, and devotes his attention to his undertakings and his friendships. These features appear in the account, which follows ancient tradition, of his conduct towards the women of the family of Darius, in his brotherly attitude on the death of that ruler, in his behaviour towards queen Nushaba (the Kaydaf of Firdawsi, the Kandake of the pseudo-Callisthenes) whom he defends against the Russians. And if he subdues the king of China, the Khakan, and the Indian king Kayd (Porus), it is to establish a deep and lasting friendship with them.
In the Sharaf Ndma particularly, the itineraries of his expeditions are Iranian and Muslim. It is in Egypt that he introduces the rule of justice, after delivering the country from the threat of the Zandj, and it is the religion of the One God of Abraham that, in the Sharaf Ndma, he makes it his mission to spread, and for which he was to eliminate from Mecca the family of Khuzaca, who had distorted the religious tradition of the Kacba. And it is through Armenia that he starts his march to the East, on the way founding Tiflis and Bardac, occupying the legendary castle of Dar Band, and finding in the castle of Saklr the fabulous relics of Kay Khusraw. He traverses Rayy, Khurasan and central Asia, to reach India and then China. He was to return to Bardac, in this same Adharbaydjan, the homeland of Nizaml, to rescue Queen Nushaba when she was attacked by the Russians (there was in fact an invasion in 946-7).
Nizami is a bit later than when you're asking about (12th century AD), but Firdowsi is right on the money.
how much detail was known?
As I think I've outlined, there was certainly quite a lot of detail that was known about Alexander's life. But, as I think you can also tell, quite a lot of that detail was known in the same way that we "know" quite a lot about the fictionalized life of King Arthur or George Washington.
As to the extent to which these details were accurate or the accuracy of the Greek/Latin sources on which they relied, I'm afraid that's outside of my area of expertise as that's really a question of Greek and not Islamic historiography.
Sources: Primarily The Encyclopaedia of Islam entry on "Al-Iskander". The Qur'anic verses on Dhul Qarnayn can be found in Q18:83-101. (I prefer the Pickthall translation if you go over to the settings.)
Alexander's conquests left such a profound impact on the culture and history of the Middle East (single-handedly creating the Hellenistic world) that by the time of Muhammad he had attained a quasi-mythical status. Even during his lifetime he was regarded by the Greeks and Egyptians (and likely by himself) as a demigod and he was equally revered by many of his other conquered peoples, particularly the Jews. In the eighth chapter of the Book of Daniel he is represented as the he-goat of Javan (Greece) who kills the ram of Persia, his horn then breaking into four little horns (representing the four Diadochi).
Because of the Jews' unique belief in an omnipotent, benevolent God, they came to believe that Alexander the Great's success must have been due to divine favour and thence developed a tradition that, because he was favoured by God, he must have been a particularly good and pious man. From this arose the belief that, after conquering Jerusalem, the Jews showed Alexander their prophecy about him in the Book of Daniel and he converted to Judaism.
Throughout the Middle Ages, the most popular account of Alexander's life came from a 3rd century AD Greek text made by a writer known as Pseudo-Callisthenes containing a highly mythologised narrative of his life which was translated into nearly every medieval language, including Arabic. This account was further embellished and exaggerated over the centuries to form what would become the Alexander Romance, in which Alexander became a chivalrous knight. He was said to have slain dragons, encountered headless men, gone to the bottom of the sea in a glass barrel and up to heaven in a griffin-drawn carriage.
The Jewish legend and the Alexander Romance were well-known in the Arabia of Muhammad's time and believed to be historical, so it isn't any surprise that he makes an appearance in the Koran under the name of Dhul-Qarnayn, the Two-Horned (possibly referring to his depiction with the ram-horns of Amun in Egyptian coinage), in Surah 18. He is portrayed as a Muslim conqueror who defeats the giants Gog and Magog (likely representing the Huns or Mongols) and seals them behind a great iron gate between two mountains, the Gates of Alexander, a legend borrowed directly from the Alexander Romances.
Medieval Muslim historians had no qualms with identifying the Dhul-Qarnayn of the Koran with Alexander the Great, as the connection was obvious and all contemporary historians, Christian, Jewish and Muslim alike, believed the same legends and identified him with their own religions. But with the rediscovery of ancient sources in the Renaissance and the development of modern historiography, it became apparent that these tales about him were untrue. As such, most modern Muslims dissociate Dhul-Qarnayn with Alexander the Great, as they now know he was a pagan idolater, and instead claim he was a separate person.
TL;DR: Yes, he was very much still known to them, albeit in a highly-mythologised form.
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