If you are really worried about the condensation you can get cans of dessicant to put in your hulls. I've seen them at West Marine. You will need ports installed for access.

If you leave the drain plugs open all the way you will be fine. I have stored both of my Hobies all winter like that. At some point in time water does condense and freeze. No damage to either boat ever occurred.

I fully understand the concern... you put many hours into restoring your boat.