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I have an aquarium with a 5 cm (+- 2 in) rock-and-clay pellets substrate. I stir it every 6 months, to remove some of algae and so on that is deposited there. That way, the water gets a bit muddy and in about 6 hours the filter takes care of it.
I wonder if there is any need to clean the substrate at all. Should I leave it alone, with all those bacteria, algae, fish poop and so on? Is my current method of cleaning sufficient or should I clean it another way (eg: using a siphon)?
The stuff in the gravel can be a source of anaerobic bacteria and ammonia/nitrogen if you let it build up too high, so it's definitely a good idea to get rid of. It'll break down somewhat on its own, but nearly all tanks with any animals will produce waste faster than they eliminate it.
I would recommend using a gravel siphon rather than just randomly stirring though: that way you're removing the waste immediately instead of mixing it into the water column. (And doing your water change.) You'd need to siphon out any of the denser solids/particulates anyway, since they're likely to settle out before any mechanical filtration can grab them.
Cleaning the substrate is especially important if you have an undergravel filter. Those will pull waste deep into the gravel, and that waste will start to block the flow of water as it builds up. If it gets too bad, the denitrifying bacteria in those spots will die back due to a lack of food (the ammonia and nitrites that you want them to consume) and oxygen.
You don't really need to stir it, all you need is to siphon the top of the substrate at most. Think of all those planted tanks having a complete carpet of foreground plants, they can not even siphon properly. While its an eyesore, but eventually the waste will break down and taken care of by the filtration system or live plants.
