Yes, go ahead and make a preload variable in every file that needs it. Each resource will only be loaded once no matter how many times you
It also makes clear what files given script uses.
Godot 3.1 can warn you if there's unused variable so in case your script no longer needs some preloaded
PackedScene you will get a warning.
Renaming a resource might be a problem since you'll want to rename all instances of file path. In Godot 3.1 there will be working 'Find in files' option that will be able to perform project-wide replace.
Both of those 3.1 functionalities are already available in 3.1 alpha.