You can always catch and punish someone, and you can block simple things like P2P or block domains and IP addresses. But I don't know of a lot of companies that actually put great amount of effort into blocking content. That's just not high on the priority list. Now with the 6 strikes, it could go up a few notches.
My guess on why copyright holders are allowing P2P traffic is that they have a valid reason to allow P2P. Probably to catch offenders who torrent their content or partner's content. And their admins are probably too understaffed to worry about someone abusing the privilege. They may catch the employees, they may not. We have no way of knowing. But I am sure downloading truly infringing content is not allowed.