a high deck can interfere with paddling, if the user is not proportionally taller.
a high deck takes more hit from wind, which, depending on paddler skill, hull shape, skeg/rudder, etc. can make for handling difficulties.
if the rear deck is proportionately high, with a high front deck, it can make self rescues more difficult.
I can't remember the details, but, I seem to recall that manufacturers have not been measuring deck height consistently. Like, some may measure just under the fron coaming. Some may measure under the deck, ahead of the coaming, or, something something.
1 Canoe/Kayak Trailer
Rescue / Throw Bags