Do the bonus still apply if my equipment is on its max level? For example, i have a sub weapon at max lvl 40, and i also have alchemy stone that has a bonus of +5, does it mean that this addl +5 no longer applies to my max lvl subweapon?

applies 

 for exemple your weapon still +40 and III not +43 two separate stats

with alch stone you will get +45 and III 

So easy to tell ffs! Did you combat power increase when you equipped it?