>My 3 deep frame obs. hive gets a little moisture on the inside of the lexan from time to time.
You need more ventilation.
> Only the two lowest frames are occupied for now. Should I ventilate the top?
Or the sides or where vever.
> Would small holes drilled in the lid be enough or must I add vent ports?
I'd put a 1/2" or more hole and cover on the inside with #8 hardware cloth. If you go on top and use #7 you can use it to feed pollen in times of dearth or late winter.
> Could I remedy this with bees in the hive?
Just haul it outside, and do it. If you like take the frames of bees out and set them in a nuc while you work.http://www.bushfarms.com/beesobservationhives.htm#working
> Shall I wait and see how it goes when the weather warms and the bees increase?
I would try to remedy it.http://www.bushfarms.com/beesobservationhives.htm#ventilation