How do I fix the duplicate libraries I think the new Photos app has made?
See https://apple.stackexchange.com/a/180313/54484

The files were not duplicated, rather additional hard links were created. The data exists once, and each hard link is simply a pointer to that data on the hard drive.

Deleting one library will not recover any significant space, because hard links to the same data still exist. Finder shows the size for each library bundle as including the hard linked files, so it appears that much more space is being used, when it is in fact not.

As far as your "missing" 33 GB, unless you have turned on the display of hidden folders you are not getting an accurate count by simply counting the size of visible folders. Use something like Daisy Disk for a true view of what space is being taken up and where.

Finally, for the record, both Aperture and iPhoto work fine under Yosemite, so long as you don't delete the libraries they used. They cannot read a Photos format library.