(Coming at this from my background as an American religious scholar.)

Within academia, there has been no tradition of self-censorship. On the contrary, accusations that scholarship is too whitewashed or ecumenical, or that scholars fear persecution for being too critical, have been fairly loud, while I'm not aware of any incidents arising from bold scholarship, nor instances of self-censorship.

Revisionist historians of Islam are so large as to make up their own school. John Wansbrough, who is famous for his extremely abtruse academic writing style, proposed that the Quran was composed not by a single prophet but by a group of different authors; following him, Patricia Crone proposed that the entire history of Islam was an Arab fabrication and it was originally a Christian heresy. Both of these scholars wrote their most important work in the second half of the 20th century when political Islam was making worldwide news, but their publications were favorably reviewed in academic journals and there was no self-censorship surrounding them.

The real problem began to arise when a third revisionist scholar, Christoph Luxenberg, started making waves. Writing as a disciple of Wansbrough, Luxenberg's work is similarly dense and abtruse, but unlike Wansbrough, Luxenberg makes some fairly concrete arguments about the meaning of Quranic Arabic. You may remember him for the "seventy-two virgins are really seventy-two raisins" theory. Luxenberg is a pseudonym, and he claimed he had to stay anonymous to avoid persecution. But there is no record that he was persecuted. Rather, the quality of his scholarship was questioned by some fairly harsh reviewers, and his work continues to be seen as dubious today. This has become part of an anti-revisionist trend by a new generation of Quran scholars, some of them ethnically Arab but all English-speaking, who generally view revisionist claims with skepticism and seek out verification.

This has by no means stopped the production of revisionist works. As one recent example, in 2017 an independent scholar named Dan Gibson made a study of the qiblas of early mosques and concluded that the Black Stone of Mecca was originally in the city of Petra and that it was moved in later centuries. This was again critically reviewed (personally, I think qibla markers were not very scientifically determined in the first few decades of Islam), but no one has objected to Gibson's right to study or publish.

Parallel to these trends in Anglophone scholarship is the book The Myth of the Andalusian Paradise, published by a Spanish scholar, Dario Fernández-Morera, in 2016. Fernández-Morera claims that there is an overempasis on religious tolerance in Spanish writing on medieval Islam. However, he doesn't produce much evidence of Spanish scholars actually exaggerating religious tolerance, as the reviewers of his book have noted. Perhaps he is responding to the rhetoric of museums or NGOs. In any case, he certainly did not avoid criticism of Islam in his book.