I've spent a lot of time to solve this issue and hope this it can help even if it's not the most common cause of the issue.
The problem for me here is to know if Photos and iPhotos store your photos twice in two different spaces of your hard drive or only one with a symbolic link.
I said that to me this is two different places (and it is not a good thing)
If you look at the sizes of a particular picture in both directories, they are not the same. Thus to me it is not the same object (a hard link would have EXACTLY the same size)
If you do 'ls -lha' for these 2 files (same picture):
You obtain these different file sizes
-rw-r--r--@ 1 doubelle staff 38199 1 jul 22:47 IMG_0762.jpg
-rw-r--r--@ 1 doubelle staff 37136 1 jul 22:48 IMG_0762_migrated.jpg
That way you can know if a file is linked or duplicated.