In a pond it is a somewhat difficult desigion regarding maintenance and cleaning.. Debri will always accumulate on the bottom, like it does in aquariums. But in aquariums we have planted substrates and do regular water changes do regular inspections and if we see pockets of dirt accumulate we can easily syphon it out and take out decaying leafes etc.
It's all about how big and how deep is your pond and what measures are you willing to invest to maintain it? Using a light colored substrate in the shallow parts of a pond to contrast the fish aint such a problem with the proper maintenance. Depending on your fish choice and substrate size the fish can also help cleaning and maintaining it.. For example a school of proper sized goldfish will turn the substrate over and shift it around constantly. I see this in my 300 litre bath tub which also has a layer of light colored pond substrate. (A not to coarse grained porous light weight material) They dig in take it in their mouth and spit it out again sideways filtering the edible stuff out of it.
Now 300 litre aint a big deal and very easy to maintain. I'm not sure if i would do the same in a 3000 + litre setup.. But it definitively doesn't need to be a problem.. It takes work and thoughts how to pull it off, it's not a drop it in and laid back waiting till problems occure and than say "Oh that was a bad idea". The best example is Amano's Forest under water setup in Lisbon.
That isn't an aquarium and it also isn't a pond, it is almost a recreation of a river. And it has substrate, tons of it..
Now if you look at the making of video from this setup you see he very cleverly integreated plantpots into the bottom.. This technique could also be very effective in ponds..
I have no idea if these ponds are artificial, i think they are.. Loaded with plants, koi carps and a sandy substrate. Thinking of it, my best guess is, the same design technique is applied as in Amano's submersed forest..
Anyway if i would recreate it, i would make a concrete basin and isntead of baskets i would integrate pot holes into the bottom to fill with substrate where the plants should be. Top the whole off with a sand in prefered color.