Played GC online for thousands of hours, The only thing I remember people doing that affected others was FSODing folks(Frozen Screen of death) and that was done by people using a certain word select exploit that freeze you in the lobby you tried to join if they were spamming it( the main EU ship Polaris 1-1 died because someone sat in the lobby for over a year staright doing this constantly)
Later on when episode 3 came out there was also a more controlled method of FSODing the entire lobby if you had a Japanese copy of the game while using a action reply to force it into English once again this was word select related.
Shop dupe /multi equip exploit was being used everywhere but don't think most people cared and the folks that wanted to play legitly just stuck together.
Saying that I might have missed some stuff near the end, I spent my last few months subbed making friends on the Japanese ships running around the lobbies spamming silly symbol art.
Also done abit of digging the folks that lost their accounts lost em to a scam rather than hack, They were giving over their CD keys for "access" to private servers.