I wouldn't say you are doing much "wrong," as some of this depends upon the specific aquarium (fish species and number, plants, feedings, volume, filter, etc all factor in).
Water changes are the most crucial aspect of any aquarium containing fish. Weekly is the minimum, and the volume can depend upon the afore-mentioned factors but in general I change half the tank water every week. This can do no harm, assuming the tap water parameters are reasonably close to the tank water, and you use a conditioner. Think the more water you change the better, rather than the opposite. Provided the tank is not out of balance to begin with (fish vs volume) once weekly with 30-50% should work fine.
Cleaning the substrate at every water change is something I do, but only in the tanks where I clean the substrate; some I do not. Depends upon plants and fish load. I generally clean open areas, not under wood or rock and around plants. I have sand in six tanks, fine gravel in another, and only in the gravel do I dig down a bit. In your case, without live plants, the organic decomposition that occurs primarily in the substrate is not really needed for anything and this can raise nitrates and make the water less habitable for fish. In your case I would continue cleaning it every water change.
As for cleaning the filters, I rinse my sponge filters every water change, and the canisters on the larger tanks get cleaned every 2-3 months. With my fish loads, and having live plants in all seven tanks, this works best. You want to keep the filter reasonably clean so the water can pass through the various media and not be blocked so it slows down or manages to bypass the media. The frequency is something you learn as you do it, and it can as I said vary from tank to tank.
I run a sponge scraper over the inside of the front glass, and sometimes the side glass, every water change even though I usually don't "see" anything. But this is best, as biofilms form on every surface and these attract algae and bacteria (good and bad) and microscopic critters, and it is best to keep all this off the front glass.
As for that article comment, there is diverse opinion on doing water changes at the same time as other maintenance such as filter cleaning and I guess substrate. I really do not see how the substrate cleaning and water change could combine to make things worse...and adding in the filter cleaning too...none of this is going to remove the nitrifying bacteria. There are other bacteria of course, but all bacteria are sticky and adhere to surfaces (filter media, grains of substrate, wood, rock, etc) and it is not that easy to dislodge them. Could you post a link to the article? I'm intrigued.
Byron.
