(Game here is Parasite Eve 2)
It didn't happen in every game but often enough that it's noticeable. They're usually not shot as straight-up titillation, instead going for a tasteful nudity kind of thing and intended to fulfill some kind of storytelling or characterisation purpose
"You see, you gotta show them being vulnerable. They may be badass, but they're still girls, after all" 
-90s game director, probably
Agreed. I had a lot of fun with Peace Walker cause it wasn't entirely up its own ass and the gameplay was great. Making The Patriots into the entire cast of mgs3 absolutely pushed the series over a cliff it could never come back from. Not only is it shallow and stupid compared to the less tangible patriots we got in mgs2 but it also just doesn't make any damn sense from a character perspective for most of em. Why the hell would SIGINT give a fuck about any of this? Same with Para-Medic.