(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
I remember reading something about Madonna wanting to make an American movie about the first game back in 1999/2000 and Square refused lol.
There actually is a Japanese Parasite Eve movie based on the book. I can only imagine how amazing Madonna's movie would've been