iPhoto to Aperture

I moved from iPhoto to Aperture about 5 years ago and have noticed that the masters for the older pictures are in the iPhoto Library in Finder and the newer ones are in the Aperture Library in Finder. Is this as it should be?

The photos will be in the library that you imported them to. If you imported your newer photo into the Aperture library, that is where they are.

If you are using Aperture 3.3. or later you could merge all our phot libraries - aperture libraries and iPhoto Libraries into one library for a mor consistent organisation see: Aperture 3.3: How to use Aperture to merge iPhoto libraries

Also, when I turned on Aperture this morning there appeared empty Project folders with the names of all the iPhoto Events. Can I just delete these empty Projects?

That is hard t say without knowing what you recently did.

Are the projects really empty? Check the search fields in the Aperture window, if they are empty or if you have any filters applied to your current view if filters are applied, the projects may not really be empty and you would be deleting photos when you delete the apparently empty projects.