Actually, the bacteria love substrate. They will colonize where the conditions they need are being met. One of these is being pretty much out of the light. So they will be in the substrate below the surface. However, they also need oxygen and this will be lacking before substrate is one inch deep. Unless one has a planted substrate with roots in it, the bacteria below an inch are all anaerobic. In fact the good bacteria will mostly be in the top 1/2 inch. But, if you are only vaccuming junk off of the surface of the substrate it wont disturb any bacteria below.
Further, the bacteria creat a bui-film which attaches to a hard surface and in which the bacteria live. Doing a substrate vac will not suck them off. The risk is in turning over the substrtae and having the parts with the bacteria on it end up deeper down when thing settle and if there is no oxygen for them where they the land, these do not last. However, once we have established the needed bacteria in a tanbk and not just in the filter, if some are lonst in one place, hey will reproduce in other places to replace that loss.
Once has to damage a decent amount of bacteria before it will have a noticeable effect on a tank. I keep a lot of plecos and it makes for dirty substrate. i regulalarly deep vac, the sand and suck up a lot of gunk and have no issues. It is not so easy to remove enough bacteria by vacuuming a tank to create a cycling problem.
So go ahead and vacuum the surface crap off the substrate.
Next, I woiuld not use either of the cycling products you did as neither contains the bacteria that will inhabit your tank when the cycling is done. Stability doesn't contain any live bacteria, only spores, and the nitrifying bacteria reproduce by dividing and do not form spores. The nitrite bacteria and how to detect them are patented and cannot be used in most products. They are in Dr. Tim's One and Only and Tetra's Safe Start (or Safe Start+). You can also rinse out cycled media in a new tank to jump start the cycle. Moving actual media or substrate to a new tank can also help to jump start a cycle.
If you run into problems or before you do, consider reading the two articles here in rescuing a fish-in cycle gone wild.
https://www.fishforums.net/threads/rescuing-a-fish-in-cycle-gone-wild-part-i.433769/
https://www.fishforums.net/threads/rescuing-a-fish-in-cycle-gone-wild-part-il.433778/