azimer has said that he has made lots of cracks for games for his own personal use. unfortunately, he has also said that they were not stable enough to release it.
on the last question, id imagine cracks do different things depending on the type of protection.
also, maybe i missed something, but i dont see how Banjo Tooie could be so good for all u people to be completely obsessed with emulating it. it may be a 'holy grail' of n64 emulation, but afaik its the only game with that type of protection/ that chip. wouldnt the effort that would go into emulating that game better spent in making more accurate emulation of the n64 as a whole?