Yes, copying a project to a new location is the quickest way to clean a single project, but I mess around with a lot of different projects over short periods of time, and like to be able to clean everything at once periodically. CakeWalk Audio Finder works well for that.
Step-by-step procedures for even the simplest operations always look more complex when written out; just try writing a procedure for tying your shoes.

Using the "Excluded Waves" folder is just a trick to allow archiving files for a while to avoid the extremely bizarre fringe case that there might be a problem down the line because your files are arranged like a madman's breakfast.

Otherwise, you can just delete them and go on your merry way.
I have a dedicated top-level "Cakewalk Projects" folder at the root of the drive with all other paths excluded from the scan. I haven't timed it, but It would guess the scan takes 3-4 minutes. I have a huge number of projects/versions accumulated over the years, but maybe proportionally fewer audio files because I work mostly with synths and don't always render every track separately, so my scan might be faster. But, yes, you'll want to move all the orphans at once because each move necessitates a re-scan. If my system took that long to scan, I would move old, unchanging projects to a separate "Archive" path that I could exclude, and only clean recently active projects.