Did type up a nice long post, but my laptop lost battery . So I'll try to sum it up in a couple of paragraphs.
Basically, no, I don't think this happens much at cardiff any more. In recent years, the hooligan element, as for the most part, disappeared. Of course, there are some idiots still around, but I honestly think we're no worse than any other championship team now. Point proved last year when most of the trouble at NP was caused by wolves and bristol fans chucking seats around.
In the past ten years, things have changed a lot. We no longer deserve our reputation IMO. Of course, the media have done their best to make sure we keep it. The FA cup win over Leeds comes to mind. Instead of celebrating a huge giant killing, the media decide to exaggerate the actions of a few mindless thugs.
Of course, its not surprising I'm saying this, of course I would. It's the club I love. And you (as in saints fans in general) probably will choose not to believe me (not that I exactly blame you, the violent minority easily block the rest of us from sight).
As for the welsh league thing, believe what you will. But the only reason we are in the english system is because your FA allow us to be. We're officially a member of the FAW, and only associated with the FA. Thus it would be easy for the FA to force us out. But judging by last years events (most notably the FA saying we would qualify for europe if we won the FA Cup), I can't see them kicking us out.
As I said above, I am horrified if what is claimed is true. I think I speak for most true city fans that we are all ashamed to have people like that associated with us (the thread on the cardiff boards backs me up). And I hope the saints fans involved are ok.