This is not an ignorant question at all! In fact, it's something that many people have asked since the game came out.

Seeing these animals in ancient Egypt might feel out of place because they are associated with the desert, grassland, bush and forest environments of Central, Eastern, and Southern Africa. Many of the animals you mention are either currently endangered or have been extirpated in Egypt.

All of these species had a larger range in antiquity, and some still have wild populations in Egypt today. If you were able to step back in time 2,000 years ago, when AC: Origins is set, you would see an ecosystem that is almost unrecognizable.

The importance the Egyptians placed placed on animals like hippos, elephants, hyenas, lions, giraffes and antelope can be seen in the frequency with which they were depicted in art, and the portrayal of gods with their attributes.

Scientists have studied archaeological and paleontological evidence to understand how these extinct populations were related to modern animal populations, but for the sake of brevity I'm not going to get into the finer points of this.

The striped hyena for example, is actually still endemic to the Middle East and North Africa, albeit in small numbers. Thousands of years ago, both striped and spotted hyenas were far more numerous and would have played a larger role in human life.

As I understand it, it is uncertain whether any cheetahs still live in Egypt, but thousands of years ago the country had a stable population of cheetahs. Cheetahs can be more readily domesticated than other great cats, and they were occasionally kept as pets.

Hippos were greatly feared and respected, possibly on par with crocodiles. This was because they are highly territorial and a hippo encounter on the Nile or in Egypt's other bodies of water could be fatal. For this reason, the fearsome goddess Tawaret (who protected women and children during pregnancy and childbirth) was a hippo. Conversely, the demon who waited to consume the hearts of the unrighteous in the underworld was a terrifying combination of a hippo, lion and crocodile. Those three animals were the most feared, and had no natural predators. Hippos and crocodiles also frequently appeared in Roman art depicting Egypt, indicating that they were considered "iconic" Egyptian animals.

North African bush elephants are sadly extinct, but they were once found throughout parts of North Africa and East Africa. They were used as war elephants by the Carthaginians, Romans and the Ptolemaic dynasty.

Some trade cities on Egypt's southern border, like Ptolemais Therou (literally "Of the Hunt") were created as outposts for trading elephants and ivory from more southerly regions. Other exotic animals were trafficked through these cities, but elephants were particularly important because of their use in warfare. The only point of inaccuracy with Origins' depiction of war elephants, is that in real life they were much smaller and less intimidating than they look in the game. This made them a disappointing investment for the Ptolemies, who found them too timid to pit against the Indian elephants used by the Seleucids. However, this is a pretty minor use of artistic license.

Archaeological evidence tells us about the way ancient Egyptians interacted with the fauna of Egypt. The Egyptians kept many of the familiar domesticated animals, like cattle, chicken and goats. They also engaged in less successful attempts to domesticate animals like the antelope and hyena. Hippos, though not domesticated, were hunted for meat and ivory. Incidentally, more modern reports indicate that they taste very similar to pork.

It was through contact with Egypt that the civilizations of the Mediterranean became acquainted with a lot of African fauna. For example, the Minoans and Mycenaeans painted baboons and macaques brought from Egypt. For a brief time, pet cheetahs (imported from Egypt) were popular among rich youths in Classical Athens. (I can't recommend vase paintings of cheetahs enough). Giraffes also appeared in the colosseum games of Rome, but the first giraffe in Rome was probably the one Julius Caesar brought back from Egypt in 46 BCE.

I know less about the historical range of the last animal you mention, a Bonelli's eagle. It might be in some of my books, but for obvious reasons most literature tends to focus on larger animals that impacted human life more directly. As I am not a naturalist, I looked up it's current geographic range online. It currently inhabits a fragmented territory spanning modern day southern Europe, north Africa, and parts of the Middle East and south Asia. (In one of the few times it's probably okay to reference Wikipedia on this subreddit) I feel the need to point out that they are sometimes found in northeast Egypt. This seems like enough information for me to conclude that Senu is a historically accurate companion for Bayek.

The reasons behind the disappearance (and shrinking ranges) of these different species are complex, but it can be generalized as a combination of human encroachment, climate change, habitat destruction and hunting.

Many of these animals (lions, leopards, hippos) are large and dangerous. Humans had an obvious incentive to eradicate them. Hunting animals like cats, hippos and elephants for pelts or ivory also decreased or destroyed populations. Climate change has exerted some pressure on the flora and fauna of North Africa, which has varying causes both natural (such as the periodic cycle of aridity vs wetness in the Sahara) and man-made (such as the deforestation of North Africa over the past few thousand years). Lastly, the development of increasingly intense agriculture and land development also destroys habitats, threatening populations.

Similar stories can be found throughout the world. In many parts of the world, we have tended to push certain species out of their natural environments. This was the fate of wolves in many European countries and in the United States (recent efforts at reintroducing wolves aside). In other parts of Africa, elephant and rhino populations have become endangered or vulnerable to endangerment. As far as I am aware virtually all great cat populations are threatened, with the exception of mountain lions. Although it is perfectly possible for human population growth and urban development to occur without threatening the native animal species, this is not always the case.

All in all, I was personally blown away by the accuracy with which the flora and fauna of ancient Egypt were portrayed. It would have been easy for the game devs to limit themselves to a more stereotypical "deserts and camels" representation of Egypt, instead of portraying the variety of its exceptionally diverse biosphere. That said, the average playthrough will include a lot more running around hacking up hippos and lions than was probably accurate.