I'm not so sure about most yakuza using karate. Some of them do Oyama style karate. Some of them have connections with very old styles of martial arts that are not public, for example a few schools of koppo.
The main weapons of yakuza are guns. They're about the only people in Japan to have them. Other weapons of yakuza include baseball bats, knives of any kind, and occasionally you get the traditional Japanese martial art weapons..But that is rare. Mostly just guns.