I can't be sure about San Diego, but here in FL, 2-3 years is pretty normal if you have a diver cleaning regularly. I'm having my bottom done now after only 15 months, but it sat without cleaning for that long.
On the exhaust, when did you notice this? Has it been that way for long? Loading the boat heavily will do that, as will water intrusion. The danger is that if your boat is sitting lower in the water, the upward incline that was designed into that system to prevent water from getting to the engine becomes compromised. Wakes and wave action on the stern are sometimes enough to push water through the muffler and into the engine. A simple exhaust flap is not enough to prevent this IF the water level is already over the edge as you are reporting. Water backing up into the engine is serious. Better check that.
"When life gets hard, eat marshmallows”.