I believe that any bacteria that we wish to keep in our systems will be firmly attached to some substrate. It is beyond the capabilities of a hydrovacuum to dislodge young, healthy bacteria. If you don t believe me please take a long hard look at a fluidized bed. Those bacteria are being sand blasted all day long. And yet they colonize at an even faster rate and occupy even less space than their counter parts in a traditional submerged biological filter.
Bacteria reproduce rapidly.
Their colonies form sheets overtop of older, dying bacteria. The grinding action limits this layering effect, insuring that only the young, healthy bacteria will survive. So please vacuum your gravel bed and don t allow yourself to be afraid of harming the bacteria. Any good bacteria that you may loose in such an action were probably attached to something you don t need anyway i.e. leftover food. I have never heard of a dedicated aquarist having an ammonia spike after doing regular undergravel maintenance.