I suppose if the ditches were below the then water table they'd have water in them. Don't know if they were a lot higher then. I've been chasing some details on water table levels in the area (Silbury's ditch seems very dry lately) and the levels have varied by very many feet in the past decades.
On the other hand, if there had been water in the henge ditches once there'd be a layer of visible silt laid down I'd have thought.