I just got done touching up my stand with oil-based polyurethane. Nothing fancy - just cheap, MinWax poly from Home Depot. It went fine with no mortality and no signs of stress in the tank inhabitants. The levels were likely not the same as refinishing the entire stand, but at least it's some evidence.
My rationale for using oil-based went something like this:
All polyurethane varnish has some sort of volatile solvent that evaporates off, leaving the polyurethane behind along with fumes from the evaporated solvent. For traditional, oil-based polyurethane, it's a some sort of hydrocarbon. For water-based, it's generally a glycol ester, although I've used some that at least smell like they have a component of ammonia in them as well.
For water-based coatings, the solvent is by definition water soluble, where as for oil-based coatings it is water insoluble. As such, the fumes created by a water based coating would be much more likely to get absorbed into the tank water and potentially cause issues, where as the opposite would be true with fumes from the oil-based solvent. I know this assumes equal toxicity at equal concentrations, etc, so it could be totally wrong, but it sounded good in my head, and in the end things went fine.