I dunno... I never put forts in enemy territory. To be honest I never send my merchants to other faction's territories except for Timbuktu, and even then I try to acquire Timbuktu for myself. I prefer to keep them in my own territory where I can shield them.

But yes, a merchant can join a military stack and still make money under their protection... And of course you can have more than one merchant attached to the stack.

I've actually found that there may not be any limit to the number of agents attached to a stack, considering that I can put more than 20 spies in an enemy city.