Vacuuming sand bed ?

Vacuuming of the substrate is a practice that was implemented because most substrates back in the day were coarse.I.E. Crushed coral for SW,Gravel or river stones for FW.These coarse substrates would trap lots of debris and would foul over time unless cleaned. Sand is much more dense and will not trap debris right away allowing inverts/fish/bacteria to consume it. Over time the sand can become compacted and this is the only reason IMO you would want to stir it and then you would want to do small areas at a time and only the upper layer.
Edit-Yeah thats alot shallower then most tanks. I still wouldn't disturb it.Just keep testing parameters and doing your WC's.