short answer: yes. clean my mac can be a bit too exuberant in removing “unneeded” files.
here’s the detail:
Stacks stores intermediate data in cache files while it’s running. this allows Stacks to use less memory while still giving access to many images and other data. the cached data gets pulled back into memory only as it is needed: e.g. like when you’re publishing or saving your project.
this is a very normal way for a media-heavy app to run and one that is recommended by apple and used by many apps.
unfortunately— i suspect in part because Stacks is not an app per se — clean my mac does not recognize these cache files as “needed” and it can sometimes remove them while they’re in use. if these files are removed while Stacks is running the results are catastrophic. Stacks loses all its intermediate data and doesn’t quite know what to do. in the worst case stacks might save a file that is missing data — especially large files: i.e. pictures.
even if that worst case is rare, the usual case is pretty bad too: Stacks will try to force itself to crash before corrupting your saved file.
clean my mac can be used judiciously and with extreme care. and, well, when automatically deleting vast numbers of files i think “extreme care” should go without saying. 
at a minimum ensure you have a good backup before letting an app loose to delete things. and on the other hand — maybe don’t let apps do that — like ever. it’s like giving Marie Kondo the keys to your house and telling her to go for it!!! 
but the point is…
so long as clean my mac is never allowed to remove files while rapidweaver is running, then it is, i suppose, safe enough, for our purposes. but that’s a lot of caveats to hang on your important work.
more blunt opinion:
you could not pay me enough to run any app like that on my own machine.
disk space is ridiculously cheap. my data is invaluable. no way. no how. nope nope nope.