Couple things:
As many others pointed out, it's most likely illegal for him to do that (depends on the state and the purpose for his being there, but from the sounds of it, this doesn't sound like it is legal).
As for the locks thing, you'd have to check your lease. Most leases do not allow you to change locks without the landlord's permission and then they require copies of the keys anyways because it is technically their property and they are responsible for upkeep, showing the place, and after you leave.
As for something you touched on early on but I've seen no one mention in this topic so far, you should really check your state's laws and the zoning laws of your area as well as your lease. While what the landlord is doing is very likely illegal, it is quite possible you running a small business out of a residential facility (especially one you don't live in) is also illegal. There are quite a number of leases that forbid this as well (in fact, my current lease very specifically states my apartment is only allowed for residential purposes... Any commercial business cannot take place within my apartment without written and signed documentation from the landlord and from the town board that I live in).
I agree with the others: you definitely need to do something about this. However, I would make sure you look into all the legalities of your lease, your local/state laws, and similar. You want to make sure you have a strong case and, if it can be determined that
you
are breaking the law/lease requirements, it can come back to bite you if you don't research in advance.
Thanos was wrong. Mike Ehrmantraut, "The moral of the story is: I chose a half measure when I should have gone all the way ... No more half measures."