How many Master Assassins can I train

I had no trouble doing all these immediately (beginning of chapter 3, I believe I did it) and in fact you can even max them all out in that chapter - unlike previous games, you can access pretty much the entire city except the very small Arsenal district from the very beginning.

What you might be missing, though, is that you can only have one mission at a time open. There doesn't appear to be any way to influence which den's mission will come up, but when you finish one, if you have a level 10 Assassin, the next one should crop up. This also goes for the level 14 missions as well - you have to take them one at a time. (Those are extra obvious because the Den Leader shows as on a mission in the assassin's interface even though they're actually still there.)

No. Not for regular missions or even if you station them in a city. They will remain den masters there and your dens will be protected. Though keep in mind, if they are killed in their missions, the den will (probably) be unprotected and will have to assign another one to the respective den and train to master. I don't know what happens in this case but you probably won't have to do the associated missions again.