There are ... uhm... issues. The problem is, the no-limits patch changes the executable, which probably causes the no-CD crack to either NOT recognize the executable (and thus not apply the necessary changes), or make changes in the wrong place (which might or might not be harmful, but in any case doesn't do what it's supposed to)...
Your best bets are to have two MGE executables, one with no-CD, one with no-limits; or to try and find another crack, or make one yourself. In any case, applying multiple patches might be tricky and screw up the executable, so be sure to make backups (of the civ2.exe).
I don't have MGE myself, and I only know other people have experienced the same problems... I don't know if there actually is a sollution.