I've been having this issue I cannot figure out. I frequently get Illustratror files from designers who work for our company and when I open them, all the clipping masks are gone.
This only happens with files from certain designers so I am led to believe it is not my settings.
I am running an up to date version of Illustrator 2021 on my Macbook Pro 2018 touchbar on Big Sur (this has been going on for over a year).
The way I get around it is I ask the desingers to embed ALL files in the ai files then the masks are there when I open the files. If the files are linked, the masks are gone. This is troublesome as the files are huge with embedded files and some documents are 100 pages.
I attached some screen caps of what the correct file looks like then what it looks like when I open it in Illustrator.