Risk of altering folder structure in Apple Photos?
Everything is named per the database and systems, so please resist the urge to move anything. 

You can secure that data with an encrypted disk image if needed or encrypt the whole drive transparently with the current FileVault scheme if that’s what’s the main concern. 

Unless you want to export out the files to disk, I wouldn’t touch it. 

The best tool for making sense / merging / duplicating photos is https://fatcatsoftware.com/powerphotos/ in my experience.