Trojan'd keygens - Is there really anything hiding there??

Being a musician, I am not always fully understanding of how things run with regards to cracked software and keygens. However, I have noticed there is some occasional disagreement over whether trojans and other nasties picked up on the odd keygen or .dll actually have any substance - ie. are these files simply flagged because they are illegal?

I would imagine I am not the only one who has this confusion from time to time, and wondered if someone with a little more experience could offer some insight? I do appreciate that it may differ from crack to crack...