In our site's File Vault, we have a folder/subfolders:
.
>File Vault (top folder)
>>> Images (subfolder)
>>>>>> Yearbooks (subfolder)
>>>>>>>>> 1967 Yearbook (subfolder for each yearbook)
...
[1968 thru 1971 Yearbook folders]
...
>>>>>>>>> 1972 Yearbook
.
Each of the "19xx Yearbook" folders has scanned JPGs files of that year's yearbook pages.

Can I create Photo Galleries for each year/book from the JPG's in those folders? Or will I have to upload them again via the Photo Gallery Creator?

Yes, image have to be uploaded again.

You can use the ones in your File Vault using JVphotocube. Various ways to display -- LINK HERE

Sample of various displays possible - LINK HERE

Can also use the images already in a gallery.