Covering your pond completely isn't a good idea, this can trap gases within the pond, poisoning or even killing your fish. A layer of ice completely covering your pond will also do this same thing. You want to ensure the water has movement, through bubblers or agitators, and make sure your fish always have access to fresh air.
Some ice is a good thing however, as this insulates your water during the winter and prevents predators from attacking your fish. Instead of completely removing the ice, create a small hole in the surface via hot water, a deicer, or a pond heater. This will mean your fish have access to air without being completely exposed to the open air and the outside cold. If you frequently see your fish coming up and congregating around the hole, this means they aren't getting enough air, and more holes or a bigger hole should be created.
