Seems a lot of people are confused about the way runes end up working, even with the old masteries.
It's not supposed to be that every champion has multiple runes to work with. Just like how not every champion is supposed to be able to build every item.
Aftershock is the rune that works for Nautilus. It doesn't work for some champs. It works for him. He isn't supposed to be fantastic with Electrocute or Phase Rush, because they don't suit his class. Just like he isn't supposed to be any good building full lethality. It's not a problem. It's just how the game works.
You could bring Grasp, but it won't be very effective since keeping yourself in combat would mess with your lane's minion control. You could bring Guardian, but it won't be very effective because you don't have ally healing/shielding/buffing.
His shield has always mainly been for the shield. The damage is for jungle and minion clearing. Which you don't do as supp.