Even if they can't see what caused the disturbance, instinct tells them to make tracks. To a fish, it is better to run from a false threat than sit still and hope that nothing bigger and hungrier is on your tail. Boats make noise, some more than others, and serious flats fishermen are as concerned with hull slap as they are with livewells and poling platforms. Pay attention to the sounds of water against your hull as you drift or pole across a flat. Sometimes, solving a noise problem is as simple as changing course 10 degrees or shifting someone's weight to the other side of the boat.
Some captains actually hang strips of burlap off their boats' gunwales to absorb wavelets.
I've seen that done in Florida but never in Texas, not even on the clear-water flats of the Laguna Madre. The guys who use burlap say they hate the hassle but love how close they can get to fish. A greater problem with boats built to run ultra-shallow is the grinding and clacking sounds they make against rocks, oyster shell or whatever else litters the bay floor. Short of leaving the boat and wading, the only remedy is to keep sharp watch for potential noise makers and steer around them. The more time you spend looking for seashells, however, the less can be spent looking for fish.