Suzuki removed a nearby part, the front lower cover, as part of the frame brace recall on the K5/K6 1000. Based on that, the bike will run slightly hotter but you won't notice it unless you ride in very hot areas like Palm Springs, CA. There will be less air flow through the radiator and that air will instead flow up and over the engine, which means that the upper engine will get dirtier faster and there will be less air cooling the headers. In general this is not a good idea but it's not the end of the world. Are you also going to remove the front fender and the hugger? Suzuki puts these parts on the bike for a reason.
The Galfer instructions say to remove the lower bracket cover, which I think is what you're asking about, as part of installing their GP brake lines on K5/K6 1000. See step 3 and item D
here. I called them, asking why not cut a slot in the cover instead. They said that they couldn't figure out how to explain that so they decided to have it removed instead. I cut a slot in mine and don't see why they couldn't provide a paper template showing where to cut. This cover is forward of the front lower cover mentioned above, so removing it may result in air flowing up into the area behind the headlight bulkhead, i.e. cluster and headlight connectors.
