Users can install software on iOS devices without jailbreaking. The most common method is resigning the software using an enterprise cert (there are plenty of sites on the internet that do this).
Yes, but how hard is Apple going to chase those certs?
Unless someone is doing something big or strategic to Apple (and random app piracy doesn't qualify, IMO), I just don't see it. Chasing "rogue" enterprise certs is all cost (time, effort, energy, risk of angering legitimate enterprise customers) for little to no benefit.