IIRC, it has something to do with grain refinement in the crystal lattice. when you melt or heat metal, the alloy component will forma solution which is pretty much homogenous. whe the metal cool or freeze, the different element will form a crystal, that is a structured crystaline lattice in which each element has a place. The more homogenous this crystal, the harder it will get. Once a crystal has frozen, element still displace within it, albeit at a very slow rate. That is why BHN will vary over time. An air cooled WW will harden a bit over 1 or 2 week then stabilise. A water dropped one will soften over the course of many years. The main advantage of heat treating the bullets is that it's a far more controlled process vs just droping them from the mould into cold water. You can also achieve harder bullets because of the same control over the temperature.
As far as sizing will change the BHN, well that's true. Only if you do things right, you will only size a thousandt or so without touching the alloy any deeper. the surface would stabilize at about ACWW BHN after a couple of weeks while the deeper alloy will stay harder. Since the rifling will bite deeper anyways, the softer layer will not pose problems.
Lastly, as been mentioned hardness is not everything. Seek a good fit to bore and know the limitations of cast in modern cartridges. If you are seeking good effect on games, you will need to use a heavier/slower boolit to make up the loss of velocity and one with a large meplat to upset the flesh enough for a kill.
Hope that help.