It's balanced in the same way that everyone is OP in their own regard, and have specific counters and weaknesses.
Flan is a truly monstrous person late game, with a single whack reaching 2500 damage and she can do that for four hits, but is completely useless against people who can dash away or make themselves immune to physical damage(Reimu, Suika, etc). For a HoN example, it's like picking Devourer against Forsaken Archer, Pyromancer, etc. The squishy types just aren't designed for fighting someone like that.
There are a lot of specific counters, and although some don't have one(Wriggle and Koakuma for example), they tend to get weaker late game but have a very strong early game, so they have to finish the game fast or they'll gradually become more useless in compared to some girls who have a bad early game but strong late game(Tenshi, Flan). There have been instances where Wriggle was just stomping everyone and pushed us to our base, and one of my allies(Tenshi) suddenly just started stomping all over the place and actually was able to push back to their towers because her late game started to kick in.
Additionally, Pestilence has a similar debuff where the target gives shared vision, reveals invisible, and reduces armor by 5/10/15. That's like giving EVERYONE a +100 damage attack AND he can stun too, which Aya can't. His even lasts longer, 30 seconds compared to her 18 seconds.
Pesilence>Aya
