When we last went to the Maldives in April 2016 we flew with Emirates on the same route you are taking.
The flight got into Dubai at 02.50 and the smaller plane going to Male was departing at 04.20 so that very small time gap left me worried but we made the second flight with time to spare so i shouldn't be too concerned.
You will probably be flying on the A380.Best flight I've ever been on.
BTW what island are you going to?
Rui attol on masfushi