Would it be preferable to delete the folders / albums (I presume photos will remain just in photos),
Deleting folders will delete the folder and the albums and folders inside, but the photos will stay, because the albums are just referencing the photos. The photos in albums are no duplicates, you can have a photo in many albums without creating duplicates of your photos.
You can manage your albums and folders independent of the search for duplicates.
Which system version do you have installed?
And what kinds of duplicates do you have? Are your duplicates exactly identical image files or similar photos in various states of edits? Photo Sweeper is one of the safe duplicate finders, that can find similar photos. Some other duplicate detectors can damage the photos Library badly, as pointed out by tygb.
I prefer to find duplicates by displaying the photos sorted by date. Then duplicates will be shown side-by-side and I can decide, which version to keep.