The anime is typically what's considered canon for this series, and in if she's raped at least once. You also have it implied that Rocky has been raped more than that, at least whilst young. In addition she's been a sex worker, stripper, and gained enough experience in prison fucking girls for favours that she threatened someone by saying that no one else would ever manage to satisfy them again (though nothing happened). The rest of the Black Lagoon probably have cleaner pasts, with Dutch being the big question mark (though I personally suspect he's a spy). Everyone in Ruanapur is broken though, they are the living dead that define the city.
Outside of that there's one part in Japan which gets rapey but nothing happens. There's also the twins who were both exploited in the past both sexually and as murderers for smut films, with implied genital mutilation. They are however as bad as it gets.
Weirdly enough this is a manga where I'd say I was never overwhelmed by the sexual violence, or the horrible nature of the setting. It is open about it, and the author executes his characters extremely well to the point that they are oft openly racist without the manga itself being (usually it's the opposite).
PS. The nun is clean though, and the Maid I'll ignore because she's by far the worst part of the series. She just doesn't fit at all, even in this action movie of a manga.