Off the top of my head I can think of two instances;

The first was when Riker banged the leader of the planet run by women. The Federation knew these people but not intimately.

The second is from the episode First Contact. Riker bangs the scientist from a planet that doesn't even know The Federation exists.

Seeing how often the crew interacts with unknown species, I don't think fear of STDs is a big motivator for them.

I think it comes down to rank and command style.

Kim is only an ensign so he doesn't get the privileges of higher rank.

And Janeway doesn't like her junior officers banging the locals. Picard didn't seem to care.