Light is most polarized 90 degrees away from the Sun. For example, at sunset the light is most polarized directly overhead. You may be able to see this without having to use a polarizing filter. As the Sun is setting, look overhead and you may notice a faint, violet, bow tie-shaped area above you that points north and south. This is called Haidinger's Brush.
Birds obviously detect polarized light much differently and more efficiently than do humans.
Experiments with caged homing pigeons have demonstrated that they will alter their behavior when, with the Sun in the same position, the location of artificially polarized light is changed. The answer is yes, and at present, this seems to be the most reasonable cause. It has even been speculated that cellular-phone use could have played a role in their disappearance. Sunspots or solar flares, which are associated with increased electromagnetic activity, are more likely culprits, but no unusual solar disturbances, such as an increase in sunspot numbers, have been recently observed. If satellites could be disabled, it's not a stretch to think that birds could be disoriented.