I am personally not a proponent of deep substrate either. In most cases there is no need. However....
The danger of deep substrates is that they can go completely anaerobic, due to the accumulation of organic matter and resulting low oxygen conditions. Anaerobic decomposition produces toxic gasses, such as hydrogen sulfide and methane, and also ammonia and nitrite as bi-producs of anaerobic decomposition. These will then be assimilated by other type of bacteria living at higher, more oxygenated levels of the substrate but can accumulate high enough to cause an issue, if the substrate is disturbed. Metal toxicity can also occur in anaerobic layers of the substrate.
However, this would only be the case in non-planted tanks or very lightly planted tanks.
The root system of plants naturally transport oxygen all around the roots and create oxygenated zones in the substrate, preventing it from going anaerobic. Plants like swords and crypts grow extensive root systems that will in time grow as long as the tank and will keep it from going anaerobic.
Planted substrates are also superior to a bare bottom or non planted tanks as they develop complex and diverse microbial systems keeping tanks stable. A planted tank substrate will also have great nitrification ability due to the delivery of oxygen for nitrifying bacteria living in the substrate. In a way, the plants also benefit from a lower anaerobic layer because due to the acidic conditions in those layers, metals(micro nutrients) such as iron are in a form available to plants.
Plants also take up nitrogen compounds directly, i.e. plants prefer ammonia to nitrite and nitrite to nitrate. Nitrogen compounds such as ammonia, nitrite and nitrate are essential to plants, and are also called macro nutrients, e.g. plants need them in big amounts which is a win win situation in fish tanks. Plants will also reduce accumulation of metals and increase oxygen content both in the substrate and water column. The benefits of plants are endless but they need care and understanding same as fish do.
So generally said, there is a truth to what you have been told but in planted tanks the mechanisms are different and you can easily turn your deep substrate into a benefit to the tank.
My advise at the moment would be roll with it as it is. But I'd advise to massively increase the planted area. Add some crypts perhaps. Once established they'll start throwing runners and create that under substrate web of roots I am talking about. Add any other plants you like. Floating and emersed plants is also a really good option as they have unlimited access to aerial CO2 and will only be limited to nutrients and sufficient light levels, which are easy to achieve.
Also, look into water circulation. Besides plants, oxygen delivery to substrate is achieved via circular flow. I touched upon the subject on post #7 in the below link. Good circular flow also plays a role in distribution of nutrients and CO2 to plants. CO2 is essential to plant health, same as light and nutrients are. In low tech tanks it is scarce and can be limiting plant growth and health.The natural way of CO2 production is fish respiration, aerobic decomposition(oxygen driven) and surface movement. Swords and crypts do well in low tech tanks as they can take up alternative sources of carbon.
https://www.monsterfishkeepers.com/...ange-without-an-airstone.715954/#post-8083356
Also, keep your filters clean. I'd recommend having a sponge on the intake as a pre-filter. Filters can also go anaerobic due to accumulation of the picked up detritus, subsequent reduction of flow rates, reducing delivery of oxygen. Also, increased detritus leads to increase in heterotrophic facultative anaerobs, which in oxygenated conditions steal the oxygen from the good bacs out-competing them for both oxygen and surface area. Heterotrophs aren't very efficient in ammonia conversion either and this leads to deteriorating water conditions.
Also, once the oxygen has been reduced sufficiently, heterotrophs start anaerobic decomposition in the filter, releasing hydrogen sulfide, ammonia and nitrite, which is the exact opposite of what one wants happening in the filter.
In terms of water changes, the more is always better, no matter the tank. The minimum would be 50% weekly. With plants you may get away with that amount just fine. But you'd need more plants...
Fish diet is also extremely important. I'd look into feeding them high quality food like New Life Spectrum or Northfin.
And one last thing, the gravel may work its way up the sand. Larger particles always end on top eventually. It is only an issue of aesthetics.
Good luck whatever you decide to do.