Hello; In an established tank the beneficial bacteria (bb) are on many surfaces in the tank. There might be a small impact if the substrate vac was done at the same time as a complete cleaning/replacement of the filter system. Even then the colonies of bb would be in the remaining substrate and on the other surfaces. Also not a large percentage of the substrate would be removed at any single water change.
At any rate I did this for a number of years with no ill effects to the tank. It was something of a chore. I believe your worry is unfounded.
haha I'm pretty good at unfounded worries. I definitely think its a good practice if done like you do it.