I use super glue to seal, but also to harden. Balsa is so soft that it gets dented and nicked easily, and that's when water gets into the bait, and ruins it.
If you're using water-based paints, the answer is definitely yes. It keeps the water out of the wood, and lets you sand the bait to get it smooth.
I have never tried rattle can paints on my balsa baits, but, since they are solvent based, I think they should act as a sealer.
But, for me, it is really important to waterproof and harden my baits before I paint them. That way, the topcoat is only there to protect the paint scheme.