As I said in my SotM Europe 2024 talk, I would like to add this feature to WaterwayMap.org. I just haven’t gotten around to it! 
I did once try to waterbody ways. It helped connect up some, but so many were relations that the map looked wrong.
The tool that powers WWM, osm-lump-ways only supports ways, and not relations. You can see from the changelog that it’s under active development, with a lot to do!
Personally I think rivers should be mapped through waterbodies, so the status quo suits me. However I want WWM to support both, to precent undue influence on mapping. I think waterway=river (with name!) is correct to map through a waterbody, but I’ve no objection to =flowline.