If you've completed Bernice's route by the time Lucifer declares you the Messiah, Sylos will be fully available to buy condoms. The other way to get condoms is to break into the school lockers, some of which have a small chance of dropping condoms.
you may be missing stuff from wandering around town then, but pretty sure getting announced as the messiah is the only thing needed to buy condoms from the drug store.
