Does fishing do anything besides fill the collection?

I wouldn’t count on a Cube use unless a recipe specifically lists fish as an ingredient. Check the fish description and the available recipes in your current game version. If neither mentions another use, the collection is the only confirmed purpose here.

For duplicates, I’d hold onto one until you’ve checked whether the game gives them a separate use, then stop keeping extras if nothing in the item text or recipes points to one. The question alone doesn’t establish that duplicates do anything beyond being more fish.