If you look at a profile picture from the side, it's the height of the boat just forward of the cockpit.
If you where size 12 shoes, you want a lot of height.
The higher the deck the higher the thigh braces will be. If the deck is too high you will not have good contact with the thigh braces and it's extra weight and freeboard that you don't need. If the deck is too low it will be difficult to enter and exit and be uncomfortable to sit in.
Cartop Kayak Carriers
URCHIN Portable Anchor