If Johann was just a victim (the crew using his place and he shut up), they would have him run his business normally as to avoid suspicion. I'm betting the reason he isn't taking even the minimal care of his original/front business (his best cuts are frozen shit, seriously?) is that he is not only involved but heavily invested into what was going on in that lab and who knows what else.
There was a mention at some point (don't remember who or when... can anyone help?) of the Crooked Man taking from fables more than just their dignity, freedom, rare precious magic items, etc. but also body parts, probably to use to make magic or whatever... the point being that it's where the Butcher's skill would come perfectly into play.
Ok, guys! Thoughts are welcome as always. Additional information and theories specially! However small, unlikely, hard to articulate, etc. don't hesitate to share!