When I bought Dalliance in 2006 there were a few Zebra Mussels behind the slotted strainer cover on the engine raw water through-hull and a lot of them on the concave aft face of the skeg that the rudder blocks easy access to; sheltered places that don't get hit with anti-fouling paint. I cleaned them out with a flexible blade and that was sort of an annual thing for a few years.
Since then, I have gotten a coat of VC onto that skeg face when it was off for other maintenance work, I now have the bottom dived about three or four times per season, and I installed a raw water strainer a few years ago. So far it has intercepted exactly one Zebra Mussel and some smaller, mostly organic debris that gets through the slotted strainer on the outside. BTW, the raw water seacock is closed if the engine is not running.
Up here of course, our boats are on the hard almost half the year, so hull growth of any kind doesn't have long to accumulate. I have not seen any Zebra Mussels at haul out the last few years, but I don't know how much of that is do to the steps I have taken or if perhaps they have reached some kind of an equilibrium in our end of Lake Michigan.