If a monster's effect makes it unaffected by spells/traps, what happens if it attacks a monster protected by Waboku or something? Does it still get destroyed?
The thing here is that the one unaffected by spell/traps is your monster.
However, that does not make your opponent's monster unaffected by spell/traps.
Protecting your monster from spell/traps does not negate a spell/trap card that affects your opponent's monster.
You could, however, make your opponent's monster unaffected by spell/traps (for example targeting with whatever effect made your monster spell/trap proof), and if you do that then the spell protecting it from being destroyed won't save it from your attacks.
"Waboku" protects the monster(s) of the player and the player who activated it. It does not affect opponent's monster at all. So what would happen in this scenario is:
- Your opponent's monster will not be destroyed by battle with your immune monster.
- Your opponent will not receive any kind of battle damage.