So far, I have 3 Master Assassins all assigned to Dens. I have 4 more assassins at rank 10, just waiting to be assigned a den so they can begin advancing to Master Assassin. However, it's no longer giving me the option to do Master Assassin missions, or assign an assassin to one of my conquered Templar Dens. Do I need to advance further in the story, or is this a bug?
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.)