Hydraulic disc brakes are now available on Shimano's lowest level MTB/hybrid groupsets (Altus, Acera and Alivio) which opens up the possibility of putting them on inexpensive flat-bar commuter bikes.
Hydraulic discs brakes are obviously more expensive, and they are a little heavier than rim brakes. They are going to give better and less variable performance than rim brakes. They do work better in the wet and are much less affected by mud or dirt on the trail or road,
Hydraulic disc brakes require less maintenance. Once you have them set up they just work and keep working without needing continual adjustment. The pads adjust themselves and there are no cables to stretch or get dirty.
Replacement pads are a little more expensive, but are quite easy to change. You do have to remember to pop them out occasionally to check the wear as they are not as visible as rim brake pads.
One downside is hydraulic discs need bleeding periodically, which is a little expensive. How often and how much is costs depends on the make and model.
Wheel removal/reinstallation is straightforward. You have to be a little careful getting the rotor in the caliper, especially on the rear wheel when you are fighting the derailleur but it's not too difficult. You also have to remember to not pull the lever while there is no disc in the caliper (or insert a special block to keep the pads separated).