I think it very much depends on the tank set up. I've been keeping bottom feeders and also shrimp and snails for years...no need to siphon the substrate in such tanks. In a one fish only tank, I think you'd have to remove all that settles over the sand because you get no natural help. There's no need to stir up the sand ever.
Just swirl the siphon over to remove the detritus bits. I think stirring the sand is completely unnecessary.....speaking from experience...The key is to make the filter flow reach the bottom of the tank, all areas of the substrate. The substrate then(due to proper oxygenation) acts as an additional powerful bio filter.
Other than that I always recommend keeping dwarf shrimp if possible as they are excellent substrate and detritus eaters/shredders...but if not shrimp(because they get wiped out by most big fish) try snails, pond snails, malaysian trumpet snails and ramshorn snails. They are excellent addition if surviving the fish. They'll deal with food/detritus excess/algae (bar ramshorns who are more of an algae eater), even if it means an oubreak of snails. But an outbreak of snails(or even detritus worms if one has them in their tanks) is better than an outbreak of harmful bacteria that tries to do the same as snails/worms due to the lack of snails or similar higher creature...and can be pathogenic.
Sand doesn't let much go in between the grains, you just need to loosely remove what gathers at the top..