Andy, I used to check nitrate levels but rarely bother these days. I would only do so when planning to introduce new fish. I'm looking to restock some tanks fairly soon, at which point I will do large water changes. Fish are more sensitive to sudden changes in nitrates rather than high levels, within reason. I never use RO water, just tap water plus rainwater from time to time. I forgot to mention that I use a lot of floating plants, Amazonian Frogbit by choice, but I also have a lot of duckweed, not popular I know, but an incredibly good plant for reducing nitrates, I just use a flour sieve every so often to scoop a load off the surface, goodbye a load of nitrates. Maybe it's because I'm a biologist/ecologist I always look at the organisms first, the fish and plants, rather than the chemical parameters. If they are healthy, then the tank ecosystem is healthy.
Matt, I don't have a problem with water clarity. I do maintain my filters properly and I just use simple ones with sponge, nothing complicated. I've changed most of my filters over to Eheim Pickup, they are fairly cheap (£20 - £25) but are a decent size and have a good sized piece of sponge, some others I had before had a relatively tiny bit of sponge and were less effective. Some of my tanks are fully stocked, even overstocked by some calculations, but that's another issue I won't go into ................. Others are very lightly stocked, that's because I moved various fish around last spring, intending to restock some tanks, but never got round to it, I'm planning to fully stock all this winter. I'm always very busy in summer and so only do major operations on the tanks between November and March. The tanks are pretty well full with plants, which means I rarely see some of my smaller fish in the open, they prefer to hide away, but I prefer them to live in a more natural way, it's fun watching them sliding in and out among the plants. I should say that I only grow easy plants, I planted quite a few types originally and let them battle it out, some thrived, some died, but I'm keeping fish not an underwater garden.
I've had mixed success with Corydoras. I bought the vast majority of my fish in one go, from a wholesaler, about 240 fish arriving in one delivery to be divided among 9 tanks, quite a day. Some of the Corydoras included in the delivery were already full grown, I'm sure they were wild collected and hadn't stood up to the transport well. About a third died off fairly quickly, never ate or looked well throughout. The others took a good while to settle, but are fine now, I have four species presently including the dwarf C. habrosus which live on a gravel bottom, they have been fine and seem to enjoy grubbing around the plant roots for food.
The two period lighting idea is quite well-known, it's one of the things Diana Walstad recommends.
All living cells need oxygen, including those in plant roots. Where the substrate is very compacted there will be very few air spaces and little oxygen available, that's why vegetables for example grow poorly on a compacted soil. Some plants can do with less than others, so around the edges of ponds you will find plants which are tolerant of low levels growing in the smelly black mud which is very low in oxygen. To a certain extent plants can take oxygen in through their leaves and transport it to the roots. The advantage of gravel is that water can circulate through it much more easily, hence carrying oxygenated water to the roots, while far less gets through sand. I'm convinced that's one reason why plants grow better in gravel than sand.
Think that answers your queries as best I can.