Protect should not stop certain secondary effects on moves

In my opinion, I get that Protect, well, protects the Pokemon. But it makes no sense for certain secondary effects to not apply, just because the Pokemon protected itself.

Examples:

Hyper Beam would still need to recharge

Close Combat still gives stat drops

Torch Song still increases SpA

Stone Axe still sets up rocks

Mortal Spin still clears hazard

And so on.

It's not like just because I protected myself, or rather blocked an opponents move, that the opponent didn't actually use the move. I don't see how if I protect myself against Hyper Beam, that the Pokemon that used it now doesn't need to recharge.

I'd say this goes for misses too. Though some things like Stone Axe could be argued to set up rocks on impact