To me, bus routes are for busses. As the vaporetti aren’t busses, I would not use them. For example there are similar public services in other places which are also mapped as ferry routes like these:
https://www.openstreetmap.org/relation/90076
https://www.openstreetmap.org/relation/2690006
They are very similar, also operated by the local public transport company and operated with similar frequency, pricing, etc.
If there is no route number on the map (Berliners have “solved this” by adding the number into the name), the better approach for me would be to ask the map style developers for support of ref.