The wiki and just overall things about this mod doesn't really say much at all, I have a room under my house where I built a pond with fish and a dock. I've stood and casted line after line over and over again and haven't gotten a single crate or new fish.
Does it have to be open water/lava/void or how does it work?

I'm 99% certain that crates are 'treasures' and can only be fished in open water (see Minecraft wiki for definition), so Luck of the Sea (and Lure of course) should help a ton getting the crates.

The wiki was recently updated to reflect where you can catch each fish. Biome, wheater, full moon and location play a role.