I use 3 gal pots and had the same concern on my first AF grow (I'm on my second). During my first grow I was more concerned with how my conservative "wetting" (not watering) may have caused salts to build up in the soil. But, I saw no evidence of that. After the plant got into aggressive vegging, and I increased the volume of water, I got some significant runoffs a couple times. That may have helped. When I got to each watering being 1 gal, I got a lot of runoff with each watering.
What I'm more concerned about is that the plants expand to fill the container while it may appear above ground like little is happening. Without runoff you can't know if you have dry pockets in the soil. For example, I would water closer to the stem, thinking I was creating a "dixie cup" root area. But, roots expand into the entire pot. Those areas may harmed the roots because it was too dry. Or, at a minimum, those roots weren't getting the nutrients they were ready for (wasted development).
It seems like a small amount of water to waste. Just for 2-3 weeks. When the plant's in rapid growth it will drink more and you'll feel more comfortable with deeper watering.