Preload
For every preloaded Resource, your application / game will take that much longer to start and you really should do some type of background / splash screen loading if using preload
instead of load
Referencing
For the centralized part learnt early that's the best option and on Godot Project start have a tool script that loads all of my preloaded info in to a dictionary from a specific folder into a Singleton
like this scheme
["file_name"] = "path/to/file_name"
That can be accessed anywhere and don't have to worry about filename or directory changes
Fragility
For the raw string path forgettaboutit
Honestly you're thinking way too much about it and can encrypt your scripts on export or even for yourself by placing them in a CSV
or JSON
encrypted of course if you like to make the extra complication of your code.
Remarks
This is not so much as a real answer but more of a fuel to ignite some ideas