Surely.
I'm on the assumpton that much of the bacteria that is growing in your tank will do so in the filter, and that which grows on the substrate will hardly be removed from vacuuming. Vacumming probably only removes large particles, not the microscopic sort.
Removing wastes from the tank can only ever be helpful - it will cause there to be less ammonia, therefore less nitrite, and therefore less nitrate. It's better for overall water quality and fish health.