RE Anti-fouling paint, most fiberglass boats that are in the water year-round MUST have their bottom painted to help reduce osmosis of water into the fiberglass hull (I would have said ALL fiberglass boats, but I have been told that Formula does not recommend their boats have bottom paint applied - I personally don't believe this but it's what I've heard). Besides requiring a different paint that adheres to aluminum hulls, the process of application would be very similar for a houseboat, and I can't imagine it would not be allowed.
There is a long history of copper being the BEST anti-fouling additive, but unfortunately it worked so well the government outlawed the best forms of it back in the 1980's (OK, there were some environmental reasons also).
I can tell you that on my painted hull, in the water for the past two years, there were no mussels present a couple of weeks ago. I wish I could say the same for the props and running gear (metal).
Summary - for aluminum houseboats to avoid heavy mussel issues accumulating, anti-fouling paint is a good option, or alternatively, having the boat hauled regularly and power washed. I don't know how the economics of the two choices compare as bottom painting itself is not inexpensive. Further, this still does not address the bigger issues of mussels in the engine intakes and genset intakes.