...during all of my sexual Badness save the rape, the man was partially/mostly clothed (fully clothed, in one case). This is fairly common in assault - they don't generally stop to take their shirts off, they want to be able to get away fast. A naked man is a man who's not planning to do anything he'll have to up and run away from, in my experience.
It occurred to me after typing that that, of course, that's not the only reason they don't get naked.
1. Power dynamic. Rape is about power, not sex. If she's naked and he's partially clothed, that's a power thing, if only subconsciously.
2. Vulnerability. When one is naked, one is very emotionally vulnerable. A rapist will not allow himself to appear vulnerable.
I find it interesting that my brain works along the logic paths that it does, though, with my first response being the almost subliminal "If he's naked, it's harder for him to run away, ergo, he's not planning to."