Yes, you can use a polyurethane based varnish to seal bamboo (or any wood) without any problems. Just make sure that you let it cure fully, that it doesn't contain any mold or mildew inhibitors, and that it is clear not tinted before you put it into the tank. Polyurethane is completely inert and harmless when fully cured. It's what some types of filter media are made of like sponges and floss.
When varnishing the bamboo you might need to remove the skin on the exposed inside parts or the varnish might not stick to it. Avery light sanding wouldn't hurt on the outside either. Urethane uses water to polymerize, so dampen the bamboo slightly with a cloth before applying it to help it bond easier.
Hope this helps.