If you're talking about those polyacrylamide gel beads that expand when you soak them in water, they won't have many nutrients in them (actually, they probably have no nutrients in them). You are going to have to use liquid fertilizer to supplement whatever nutrients they need. I wouldn't suggest you use them to start
seeds, and I have never seen anything grown to maturity successfully in them (though my mom is trying to grow
peppers in them :S) You're on the right track about the
seedlings being confused.
There are two factors that come into play: light and gravity. Any plant cell that gets exposed to light will turn green and start making food for the plant. Once these cells are green, they will become the first bits of stem and leaf.
Plants know to grow against gravity and let their roots grow along gravity (down). Once the root comes out of the
seed, it will automatically reach down, and this is set as bearing to the plant what cells need to become what.
I *think* so long as the
seed stays in one position the plant won't be confused enough to not know what cells become what parts, but I'm really not positive. If you decide to try, I would cover the vase with a sheet of paper at least until you see roots on the bottom.