The beneficial bacteria are not water borne as they attach themselves to hardscape - filter elements, substrate and decor. Water changes do not really reduce beneficial bacteria.
Frequent water changes (assuming proper temperature) are not really necessary, but are not harmful as fresh water really can't be too fresh. The only exception might be to begin doing large volume water changes in a neglected tank such that there was a dramatic change in water chemistry that might shock the fish.
Our objective in weekly water changes is to do a volume sufficient enough to dilute the pollution and keep the water fresh. With advanced filtration, proper stock levels, feeding, tank maintenance and sufficient plant life, volumes can be reduced, but WWC's are still required.
As to the question of too clean, I feel it may be possible to clean a filter too much. The filter houses decomposition bacteria that break down detritus as well as BB to process ammonia and nitrites. All bacteria colonies function best when undisturbed. Although we don't want the filter to be neglected, it is beneficial to let it run without disturbance until it's necessary to be cleaned. The time interval varies widely from system to system.
Likewise this is true of the substrate, at least in a planted tank. Again a comprehensive eco-system lives there that functions best when undisturbed. However, it may be necessary under some circumstances, especially the unplanted tank, to aggressively gravel siphon to clean out decaying matter.