$1/2 game. In this hand Villain has ~$160 and is a younger guy maybe 22-24 with headphones in, haven't seen him play much but from his physical looks alone he seems like he is maybe pretty good at poker and poker is the only thing he has going for him in life...Hero has ~$400 and is 24 years old new to the table.

I'll preface this by saying maybe this spot is super straight forward and is always a shove, but I'm fairly inexperienced so I am posting just for confirmation and I'm curious how others play it...

Hero is in CO with pocket 5s. Folds to hero who opens for $8. Villain on button raises to $16. BB calls. Hero calls. Flop is 5s9s6s. Hero checks, Villain bets $40, BB folds, Hero shoves for ~$110 effective. Pretty standard right?

Very standard shove. Nice hand

Yup. He should have a lot of overpairs in his rage here, and few flopped flushes. You can't just call, as another spade will kill your hand or your action. Even if he has AsKs, you have 34.5% equity. With $88 in the pot before you shove, your $144ish will only be 38.3% of the pot, so you're close to the right price even if you can see his nut flush.

Yes definitely a shove here, especially from the preflop 3-bettor. You're just about as likely to be up against one high spade as you are a flush. You'll always have 2 shots at your boat if you are behind. I'd be more worried in a limped pot or a one-raise pot.

Sounds good to me

The only thing I would say is that the check on the flop is a little risky as you don't want it to check through. Betting out on the flop would be a good option if you weren't confident of the villian betting...