I've seen it done several ways. No doubt the cabin is a dryer environment. If you are a serious performance guy (like most people here) be aware that weight carried forward of the CG may slow your boat down. Under the back seat is probably a good compromise.
I have run an Audiobahn amp in my engine compartment for years with absolutely no issues (heat/water/etc), however that may not be true with every boat. I have a friend who installed a big system with the amp in the cuddy and he swears it has slowed his boat down. I think he is correct. My portapottie installs on brackets under my v berth. Whenever I have it onboard, with water in the upper and/or lower section, it knocks 1 to 2 MPH off my usual #s.
FYI,
Steve

I've seen a really nice fountain for sale on here with a few amps installed in the engine compartment.

We did it for years and never had a problem, although the amps we bought always had large cooling fans on them.

I have 2 Sony marine amps in the engine compartment. They are mounted pretty much to the rear seat back. The "marine" part of the name makes me feel a little better about the environment they are in. In a 25' boat you run out of room real quick, especially since we treat it like a camper and like to stay out all weekend.
Three years and no issues... knock on wood.

I have my amps in the cuddy. I use a storage Capacitor to compensate for the wire run.

I just got done installing my stereo , and it was a real pain in the ARSSS ...... I ran 0 gage power and ground wire from battery to cabin. Wanted to install under back seat but did not want to give up easy access storage. I opted to throw a box in my extreme bow as well with 3 twelves in it . (its heavy as hell) I wonder how much mph I'm losing ..... Just do not know if i can get the same sound by putting subs in the cockpit..

The fore and aft CG on a boat is like the pivot point on a see-saw. The further forward the weight is from the pivot point (CG), as well as the total additional weight, the more it impacts lift. More wetted surface =s more drag. Unfortunately I think you will see a difference.
Conversely, weight carried aft of the CG will have less performance effect. It may cause some additional drag as you are increasing your total weight to HP ratio, and some additional bowrise during plane off.
But it sounds like you have a kick azz stereo system that will make the young ladies shake their azzes .
Regards,
Steve

Just installed Eton ecc 300.2 car amplifier in engine compartment.
I have only this dry place in my sea ray 185.
I hope It will work well.

No problems here with amps in the engine conpartment

Thank you. I'm going to test my installation today.