Thank you all for your replies !
You can actually delete the gltf-files without any problems if you first create a .tscn, and then click 'clear inheritance' (on the root node).
If you create materials in Godot (as opposed to importing them through the gltf) and save animations to file, there are no other dependencies ...
It sometimes seems easier to use assets this way, especially if the scenes need a lot of other nodes (for player interactions). In the past, I have had lots of problems after a gltf reimport (nodes having the wrong transform or being deleted) ...
So yeah, still not entirely sure about this.