I'm not altogether sure Bomber-kun ever really reported the crimes and thus Judgement was ever really aware of the fact he got his money robbed every day. It seems to me he has lots of malice and the kind of mental condition and thought process that since Judgement isn't (magically) fixing his problems like it would in an ideal world, it's a complete failure and has personally betrayed him. I'd even go as far as saying the dude had a martyr complex that had been fed by the constant bullying.
I also don't believe that Misaka doesn't trust the system. Her actions are more like a combination of her rather competitive and aggressive nature and the fact she's so powerful she rarely needs anybody's help. When you always win your own fights (and even help others in theirs) it won't occur to you somebody in reality should be doing the fighting for you. However, she has shown she respects Kuroko's work and encourages her in it.