That's a shame WolvesRaven I'm sorry
It sounds like there was something a but 'funny' going on with them, both being runty (you said they were the smallest?) and losing their fur. Without a PM it would be impossible to tell. It may have been some kind of genetic defect, I seem to remember that these were pet hamsters that you bred, so you don't know the ancestry if this has happened in the line before? My only advice now would be to not breed from the parents again.
I don't think they'd be hairless, the hairless gene in hamsters is "true" hairless, where there is a default in the skin so they don't grow fur, unlike the double rex "hairless" in rats when they can sometimes have fur and then lose it.
Like you said at least they were spoiled whilst they were here, it doesn't sound like you did anything wrong with them.