Almost every base I attack now is going to have placed a banner in every corner, sure, they're one hit, but if you forget about them or use all your units too early there's basically no way you'll get a 100% even if everything else in the base is destroyed.
They have no use, are only 1/400 (forgotten) credits to build (so accessible at level 1) and were meant to be cosmetic, so why should they prevent us from getting 100%s?