Good question.
It must run for at least an hour or two during EMH since that what it would do after normal hours anyway. It probably also runs a little after EMH as well, since not every onsite guest will use onsite transportation to get to MK. What I do know for a fact is that you will not be stranded. If you get to the front of MK and it isn't running (nor the monorail), ask the nearest CM and you will get to TTC somehow.