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A file storage convention (e.g. a new LDraw/Items folder) would impact tools that don't have the capability to extend the search path through a configuration file.
To solve this issue by file storage is the best solution in my eyes. Depending on the application we also do not need to care about existing models that are build with itemID parts.
The idea of a prefix is not my favorite. If I have the booklet from TLG I am searching for that number that is written there. We should not make it more complex than necessary. If we have a different storage place it should be possible to handle that smoothly.