We reached out to Audrey Kropp of Cornell Cooperative Extension Columbia and Greene Counties for some insight. She said:
Hi G.,
Your instinct about the habitat value of the leaves is spot on. Leaf litter naturally accumulates in woodland pools providing a variety of functions. It serves as important daytime cover and helps retain moisture in dry periods. The leaves also serve as habitat for the invertebrates frogs and salamanders eat. In this man-made pool, the leaves are providing natural substrate and may actually help create a more suitable environment for amphibian breeding as well as habitat. There is not a concern for harm from decomposition, so I would advise leaving the leaves, which will likely enhance biodiversity and habitat quality. Thanks for your question and thoughtfulness.
Best,
Audrey