I agree, the leaves will decompose over time but that is natural and not a problem. It is another source of food and organics.
One suggestion I would make though, and that is to introduce some floating plants to dim the light. The fish will appreciate that. As is shown in the small photo of the natural habitat in your first post, the amount of light getting into that water is very little due to the canopy. The best way to create that in the aquarium is with less overhead light and/or floating plants. These would obviously benefit in other ways too.
I very much like biotopes, except for the absence of plants which is very natural I know. Few Amazonian streams have aquatic plant growth. My desire for plants causes me to veer away from authentic stream biotopes and have more flooded forest biotopes or geographic habitats.
This is a fine example of a natural stream biotope. Very well done.