Re: What to do with half capped super frames
My personal opinion would be to choose option 1. My understanding is that at least a portion of bees in a winter cluster are inside empty cells (the cluster more compact that way). That means that there is always empty space in a hive, and while the cluster may be warm, that empty space is not really warm.
IMHO, the value of that food in the super outweighs the possible negative aspect of that less-filled space.
And regarding Option 3, its not that uncapped nectar has a higher sugar content. The issue is that it has a higher water content. The extra water is what allows fermentation (spoilage, unless you are making mead).
-- Victor Hugo -- "Common sense is in spite of, not the result of, education.”