Zapdos vs Kyogre

Against Kyogre specifically I would want Zapdos to have Thunderbolt. One-bar charge moves are a big risk when the boss might one-shot your pokemon before they get to use it.

Try to get Thunderbolt. I was in the same boat where my Zapdos all knew Zap Cannon, but I took the risk and it paid off.

Zap Cannon, in addition to being a one-bar, also has a very late damage window, and with Zapdos' relatively frailty compared to Raikou, as well as its weakness to Blizzard and lack of Electric-resistances, shouldn't be pursued.