It's kinda annoying crafting these items and then having them clutter the inventory afterwards.

Something like what the Wire Shortcut (https://mods.factorio.com/mod/WireShortcuts) mod does for wires would be an excellent QoL - instead of waterways requiring crafting and cluttering the inventory, just make it so they are created for free when chosen from the shortcut, and they never go back and appear in the inventory, they just get deleted from the map if deconstructed.

Seconding this rather than opening a new discussion.

As an alternative, setting the waterways to disappear or be destroyed when dropped would also be good.

Good idea! Added to the list of future features.