Your bonnet will be fine with the sound proofing off, mine's been off for about 18 month with no problems.
 
I'm very very happy with the noise my car makes with big JR cone filter and soundproofing under bonnet removed, I'm running standard Bosch. It sounds a lot better than I thought it was going to. A very audible, crispy yet subtle tshhhhh when coming off the throttle.