Whether/how much to gravel vac, how deep and how often etc depends on a few factors, plus some personal opinion.
Gravel, sand, or planted substrates need different maintenance. So you'll get different answers depending on substrate.
Digging a gravel vac into a planted or dirted tank substrate might cause an ammonia or nitrite spike for sure. But not into gravel or sand.
On sand, depending on how good the filtration is, what the flow in the tank is like - if the flow sweeps most of the detritus to the filter intake, might never need to vac sand, since things like algae wafers and uneaten food don't sink into the sand as much as they do with gravel. Although especially if you have fish that dig, like cories, some does get down there, without usually causing a problem.
Live plants like some mulm, so even with gravel, no need to try to keep it immaculate and remove every trace of mulm, or disturb plant roots. Can use a small gravel vac for working around plants, you don't want to disturb their roots too much.
Mulm is basically organic matter breaking down. Bits of plant leaves/roots, uneaten fish food, fish poop etc, botanicials etc all being broken down by bacteria and "little buggies"
@Seisage 
the way earthworms and bacteria break down leaves and muck, turning it into good compost and soil.
Most of those little buggy critters and bacteria are beneficial, or harmless, and some mulm is fine, and expected, and provides plant food, as
@GaryE mentioned.
It's a mini ecosystem, so you can't and shouldn't try to make the substrate and tank immaculate and shiny every week. While it's an artificial ecosystem we're creating, there are a lot of natural processes going on at a chemical, biological, and microscopic level.
Problems arise especially in unmaintained gravel tanks if too much organic waste builds up. That can overload the system, allow bad bacteria to thrive, or things like problem algae, or cyanobacteria, which is pretty nasty stuff. So if a tank is overfed, over stocked, doesn't have many or any live plants helping maintain water quality and using up the nutrients in the mulm, if the tank isn't maintained well or cleaned at all and waste continues to build, if it's under filtered, doesn't have much flow etc. Things can turn toxic, and since more detritus tends to build up in gravel, and most people begin with gravel, you're better off gravel vacc-ing waste, making sure not to overfeed, but no need to go crazy with it and suction the entire tank every week. sweep the surface, dig into areas that need it, leave the bits that don't. Do a deeper cleaner on one half one week, then the other the opposite week, whatever system you settle into.
There is some fear about very old tanks that haven't been maintained much, or have really deep gravel beds that haven't been disturbed for a long time, being disturbed like suddenly stirring up pockets of anaerobic bacteria, which could poison the fish, apparently. But in your new set up, that's incredibly unlikely, requires a deep and undisturbed for a long time substrate I think, and there's some debate I believe about how often or likely it is to occur in an aquarium setting. The chemistry whizzs and more experienced folks like
@gwand ,
@Essjay and
@Seisage would know a lot more about that than I.
Over feeding the tank, under cleaning it, or even over cleaning it, like people who rinse everything, including gravel, under the tap (or with soap!!) because they want it nice and clean looking, but wipe out their beneficial bacteria colonies and can't establish a cycle. There's a happy middle ground.
), so the only "aerobic" sediments are at the surface (extending down to maybe 1-2 inch depth) and the edges of animal burrows. It stinks to high heaven since the bacteria produce hydrogen sulfide which is a rotting egg smell. But, well, animals like worms, clams, crabs, and shrimp dig in it all the time and aren't harmed. It may be worth taking precautions in the closed system of an aquarium though.
