The covers do not interfere with the detector, they are used to protect the coil from hitting rocks and against scratches and cracks. If you do not clean the dirt and sand out that gets under the coil, that can interfere with the detector but that is what is interfering, not the coil itself.
I don't use coil covers on my coils that I use for waterhunting, instead I use a Loctite marine epoxy, they are much easier to clean.