Mikael at Candela, the hydrofoil boat maker, here. Yes, that's a key difficulty that has to be solved by using sensors that detect flight height, and distance to the waves, among other things. If the foil leaves the water, you ventilate and come down. We use a flight controller, a kind of computer, to perform these calculations. Some sailing boats have wands, ie a mechanical stick that detects waves in front of the boat,, but using ultrasonic sensors and adjustable hydrofoils is a way more accurate solution. Check us out here: candela.com

This is explained on wikipedia: https://en.wikipedia.org/wiki/Hydrofoil#Foil_configurations

Basically, yes, for fully submerged hydrofoils you need to make sure you don't get too high or low. For surface-piercing you don't, they self-stabilize.