According to the changelog, this was introduced in 0.0.31: "changed waterways to not cost any resources and stack to 1000".
For my part, I'm quite comfortable with that change. After all, waterways in this mod are just an abstract concept -- they are needed because there is no place for ships in vanilla Factorio, and this mod uses the mechanics of trains to simulate them. However, you wouldn't expect any material waterways for ships to drive on, in real life. Granted, there are cable ferries (cf. https://en.wikipedia.org/wiki/Cable_ferry) that use cables to move and guide the vehicles. According to the article, "[c]able ferries are common where there is little other water-borne traffic that could get snagged in the cable or chains, where the water may be too shallow for other options, or where the river current is too strong to permit the safe crossing of a ferry not attached to the shore."
In other words, they make sense only for rather short distances and straight crossings on a river -- but you wouldn't use them to navigate your ship across the ocean, or between an on-shore port and an off-shore oil rig.
On the other hand, the stuff that is real does cost something in this mod: I'm thinking of the buoys here, which correspond to the railway signals, or the ports, which actually are train stops. So, just be happy there are free waterways and enjoy your ships! :-)
