Yes it will affect air circulation by adding resistance to the flow path. How much will it affect the air flow, you'll have to find out. I'm not familiar with the material it is made of. Therefore, it will affect your temperatures, but again, with out that material in my hand to test with, it is hard to say by how much.
If you want dust protection, first try locating the tower off the ground, prop it up a few feet, dust tends to settle at the bottom of the room, and placing a tower on the ground makes this dust accumulation worse.
Then, you can take a look at the air flow path, depending on your case and configuration. Try to have a higher amount of intake volume of air than exhaust, so that air that enters from the front, all leave at the back with no additional in takes from the bottom of the case or rear of the case. This streamlines your air flow and reduces dust accumulation.
Then, if you still need more, you just need the intake side protected by a thin filter that you can remove and clean once in a while, not a whole cover.