Polarisers have a place in some aquatic photography, especially when working in research tanks with a mix of daylight and strobes, and in certain circumstances where coverage of a large tank is concerned, but often, it could be more of polarised light sources rather than simply plonking a polariser filter in front of a lens. By 'large', we're talking about over 15 or 20 feet wide. There again, some pros have shot tanks large enough to contain a small whale without polarisers. It all depends on the shooting conditions.
Two absolutely crucial key factors in any form of controlled aquatic photography are:
1) Light (control, direction, quality and amount) and
2) Shooting from an absolutely darkened/black environment.
Needless to say, water must be as close to perfect as possible because millions of small particles, dirt etc will float around an active tank. These will be picked up when shooting.
If you're getting backlit reflections (from the photographers side, side of tank etc) shooting a home tank set-up, it simply means that some form of light is bouncing around outside the tank and is being captured. I seriously doubt if a polarising filter will help, except to cut down even more precious light.