Hardboard is a common name, with the little holes folks know it as pegboard. Masonite is a name brand, I don't know how many different manufacturers produce it or if they are all equal...I should be a little careful recommending it as I have not used it extensively myself.
Kirk Webster and Michael Palmer have been making division feeders with the stuff for years. I got a few of Kirk's old ones in the nucs I bought this spring, and they looked and continue to hold up well. So it does have a proven record in hive use. I believe all the common adhesives work on it but I do NOT know that.
Spores are always present everywhere. The conditions required for fungus to become established are a bit different (more specific) than the conditions required for it to grow and thrive once established.
So if you accidentally use a piece of wood that already has fungus growing in it, even if presently dormant, it doesn't take much for things to go south quickly.
I doubt you will see the super rapid degradation in all your luan work that you did in those nucs.....you got a bad sheet, all the pieces from that sheet will be iffy. A better, uninfected sheet will probably hold up longer....
Broadly speaking rot resistance comes in 2 forms: chemical and density. Many species of timber have natural rot resistance from extractives(chemicals) they deposit into the wood as they grow:Cedar, black locust, osage orange....
Density comes into play with regard to your points about O2 and water. Simply put water and o2 migrate more slowly in dense media and this slows down the rate of fungal growth.
Luan is a species that has no inherent rot resistance chemically and is extremely low-density...so it gets the double whammy
I really can not speak to the long term rot resistance of the masonite...I wouldn't expect much, probably on par with Pine, But it is relatively dense and absorbs water very slowly. And as you mention it has been heat treated which at least starts it with a "clean slate".
Failures are a drag but at least we can learn. I wish I had mentioned my reservations on luan to you this past summer, but it seemed presumptuous since you had been making these for awhile and I was "new to the scene".
I really can't think of a good "fix". Most of the applied fungicides are also pretty toxic to insects. You might try to "salt" the surface with strong saline solutions...but I don't know how the bees would like it, nor how effective it would be (it is usually done with prolonged immersion in seawater). Surface films (paint ect) won't stop rot, but they can help keep it from getting started, or at least slow the "Seeding" by spores. Ultimately good air circulation is necessary to keep Moisture content down unless the material is inherently rot resistant.
Hope this helps. It is a bit of over simplification but probably still more than you wanted to know!