Tank cleaning....more importantly substrate cleaning!

Hi all I have a question, hopefully I am not repeating an old question that's been answered before.

As most of you know I have a well planted tank, with sand substrate, I have white sand and sachems black sand. When I do my maintenance clean I have only Been scooting along the top, not penetrating the sand too much. My question, if I don't penetrate the sand while cleaning does it build up with toxins produced by waste? Does this become lethal? What do most aquarists do if they have a planted tank like me?the black sand was extremely hard to clean, in fact it couldn't wash clean, so I put it in anyway it has settled as you can see from my photos but when I do disturb it or the Corey's dig down into it it does lift quite a bit of dirt/ dust like substance up but eventually it clears again, your opinions, advice would be great.

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