Not a scientific report, but of the beeks I know in MI, we have had very low losses this year. That after losses of over 60% in most in the State last year. It has been a mild winter (for us) with very few arctic blasts here. Just a few nights down around 0F.
As to the original poster, it kind of sounds like you did everything right, so I’m not sure if anybody will have definitive answer for you. I’m sure you’ll get the usual inquiries about mite counts, treatments, stores, moisture, bad queen, nosema, etc.
I would suggest next fall that you find another beek or two in your area to take a look at your setup and see what they say. There might be certain configurations that do better in your climate than others. I would worry myself about limiting the colony to a top entrance (breathing hole) that is only 1 bee space big, but I have no evidence that would kill a colony. My jumbos also just have just a top entrance in them, but it is 50mm x 9mm (2” x 3/8”). It gets pretty cold in Michigan too, but these hives are booming with bees right now. Personally I don’t think that much heat is lost through a 50mm x 9mm top entrance. Well, at least not enough to affect my bees.
What worries me about your story is the lack of bees (dead or alive). It sounds like you went into fall with a boat load of summer bees, but those bees die off quickly in the fall. It’s the new bees the hive broods up in late summer/fall that survives until spring. Those are the important bees. So maybe something went amiss during your late summer and fall brood cycles?