Far Cry has been a series to test the waters when it comes to nudity in the past. Far Cry 3 players risked getting stabbed in the chest in the game's bad ending just to glimpse some boobs, for example.
In Far Cry 4, both male and female nudity was on display, but as spotted by members of the Far Cry Reddit, it appears this has been scaled back. A modder in the community, Lord_Antheron, added some more detail, saying that changes were made to the game's visual and audio files.
They note that the Yuma model wasn't changed, just her chest is now covered up. The same is true for Kalinag. In the Shanath Arena mission, Ajay now has a loincloth covering his genitals, too. There was also a patch for Far Cry 3 on the 31st of March, but we haven't yet seen if this also made similar changes.
Right now, we're not sure why these changes were made, but speculation points to stricter censorship coming in thanks to a deal with Tencent announced recently, wherein Ubisoft allowed the company control over the Assassin's Creed, Rainbox Six, and Far Cry franchises.
UPDATE: Ubisoft has since responded to Gamereactor, explaining the issue and confusion was caused by the Japanese version of the game being accidentally released to everyone. Check out the statement below for a full explanation:
"The update you saw in Far Cry 4 happened because content made for the Japanese version (which includes some censorship) was accidentally released to everyone on Steam.
There's no intention to censor Far Cry. This was strictly a mix-up related to regional files, and nothing more.
The issue has been resolved and the proper files are now back in place. Try restarting Steam if you're still seeing anything odd."