Thank you!
1. The girls use contraceptives to make sure they don't get pregnant, it's nothing strange since the game's set in a modern time.
2. No downsides, at the moment all it is, is a "tag" that she's pregnant. Pregnancy hasn't been implemented yet.
3. That is a minor bug with the hint, the option to ask her on a date will appear after a certain big point in the main story.