Hmm, that's a good question that I didn't really think about. Here's an article I found from natgeo that explores the floating solar panels in Japan, which briefly mentions potential ecological issues surrounding their use.

Since companies must follow local environmental rules, these solar plants are usually in the center of the water, away from banks rich with flora and fauna. Plus, companies might prefer building in man-made reservoirs instead of natural ones, as the chances of harming the area's biodiversity are smaller.

tl;dr they know it's an issue and they'll try to be careful about it, but it's not stopping them from trying it out first.