Well, if you are running the amp near it's full power often, then the 'silent' fan does not push the volume of the air of the original and you can expect over-heating problems. That is an issue when doing these mods for home use. But very rarely does anyone push these amps at high power on a continuous basis (high power output usually only occurring during short periods) in the home environment.
If you need a lot more continuous power and a silent amp(no mods needed), the Yamaha P7000S outputs nearly 1000 watts x 2 at 4 Ohms, both channels driven, 20Hz-20,000Hz. If you need a bridged mono at 4 Ohms, though, the Yamahas are not intended to drive 4 Ohms bridged.
-Chris