Our family left all of our boats in 8 months a year. Bottom paint, no issues. Take them out for winter and clean them up, reapply bottom paint as needed. This was up north, (green bay). Didn't see any ill effects a good cleaning didn't take care of. Dad left his boat in lewisville a year at a time, no problems with that. If the dock hadn't collapsed on it last year, it woulda been fine. That being said, algae growth and staining can definitely occur. As far as saltwater goes I have no idea. Hope that helps.

Zebra mussels?

Yes,it will hurt it. It will get Gel coat blisters. Boats get blisters by just sitting on the wet trailer bunk boards over time. The moisture doesn't dry out very fast between the board and the hull and boats eventually get Gel coat blisters in that area. Imagine one that sits in the water 365 days a year;)