One forum member recently asked about houseboating in saltwater places like Florida:

mimoo: I am DYING for a houseboat. In a perfect world I would have one of the houseboats that they have on the lakes that are on pontoon hulls with the slides on the back. But I realize that isn’t practical in salt water. Has anyone done this? My dream boat is a huge houseboat. I just don’t know if our waters around here will allow it. We live in the panhandle of Florida. The boat would be kept at a marina.

GoVols: There's an 80-foot Sumerset in Harbor Bay, Destin, Fla., that's been there for several years. I was at the West Marine store nearby the harbor and struck up a conversation with the clerk about that boat. Very surprisingly, he and a few other guys were commissioned to sail that boat from somewhere in Texas through the ICW to get to Destin. He said it was the scariest thing he's ever done and wouldn't do it again. They ignored a storm warning and figured they'd be fine on the ICW, but apparently waves were crashing over the front porch regularly and the captain had the Coast Guard in constant contact. They got tossed around a lot and had chairs and tables fall over...What's more, when those giant cruisers would fly by on plane, they'd throw a tidal-wave-like wake, which would break over the bow of the houseboat as well. The owner only takes the vessel out to Crab Island by the Ft. Walton bridge when he wants to party, so it never navigates much more than one nautical mile from dock to anchor point. 
The clerk told me that he's doing the maintenance on the boat and regularly changes out "tons" of anodes that line the entire hull and outdrives to prevent galvanic corrosion. 
Having an aluminum hull in salt water can be done, it's just a LOT more preventative maintenance. Also, your resale value will tank as not many wise boaters would want to mess with it after that.

OLD HOUSEBOATER: Fiberglass houseboats don't fare any worse than fiberglass cruisers if you change out the deck hardware.

BananaTom: I had a 36-foot Gibson in Pensacola, kept it a Bahia Mar Marina on Bayou Chico.

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