Splatoon 2 has dynamic resolution capped at 720p as far as I'm aware. It drops as low as 548p in HH mode to maintain performance.
The Switch HH is still stronger than WiiU and we've seen games WiiU ports perform better in HH mode compared to docked. So if Splatoon could run at a perfect 720p on WiiU but can't maintain that in HH something demanding is obviously going on. Not sure if they changed the ink physics or what.
It might also just be what others have already mentioned, that resolution optimization seems to be pretty low on nintendos laundry list and they are prioritizing other things in order to get the game out as soon as possible.