I think the answer is pretty clear and is implicit in things you've said. Yes: something dangerous can be beautiful. Tigers would be a widely-accepted example. "Dangerous Beauty" isn't just the name of a movie that got a 70% fresh rating on Rotten Tomatoes. It's an idea that's something of a cultural touchstone.
Maybe the perception of ugliness evolved to keep us from danger, or maybe the story is more complicated than that. (I'd strongly suspect the latter.) But however things evolved, the concepts have long since come apart. If someone commented on the beauty of a tiger, and someone else tried to correct her on the grounds that tigers are dangerous, a blank stare would be an appropriate response. We find the appearance of tigers beautiful. They'd look the same way if, somehow, they magically became the protectors of humans. We also find their movements graceful; same comment.
The second question you ask is whether non-dangerous animals that we find ugly might actually be beautiful. The first point is that the mere fact that they aren't dangerous wouldn't be enough. However implausible it is that "dangerous" implies "ugly," it's even more implausible that "not dangerous" implies "beautiful." The reason is simple: that's not how we use the words. But perhaps more importantly, beauty seems to be a response-dependent property. The idea that something might genuinely be beautiful and yet no one—not even careful, disinterested observers who've taken the time to look—find it beautiful strikes me as very close to unintelligible.