Plexi-glass (acrylic) absorbs water vapor. The side toward the tank will be in a higher humidity environment and will absorb more water vapor than the side toward the room. The side toward the tank will become larger because of the water, and thus will warp down towards the tank. If you make them symetrical - without handles or handles on both sides, then you can flip them. By flipping them, the wet side will dry and return to the original size and thus straighten. But in time, the lids will warp again downward.
Acrylic is easier to work with, but I prefer glass lids in the long run. (I have made both.)