I believe I am correct when I say (and I'll defer to
@brandon429 judgement here too) when I say that standard tank maintenance, especially the standard vacuuming of sand bed will NOT remove and/or harm beneficial organisms within the sand. This bacteria is quite hearty and durable and would tolerate nearly any cleaning.* (not chemical cleaning such as bleach, but that's not standard)
In really deep sandbeds, ones that you can facilitate anaerobic bacteria, you could theoretically expose those by stirring up sand and thus reduce bacterial numbers, but short of REMOVING the substrate (and thus the bacteria with it) you are not likely to unbalance the system.
That being said, cleaning up the sand to remove free-floating detritus and diatoms is a good idea for sure.