The delete and update hooks are applied to non-pdf files

Thanks for reporting the issue. There is a file_exists check in PDFPreviewGenerator ::deletePDFPreview already, is this not working? What does the log message say?

Ah, yes, we are on the official release 8.x-1.1, that doesn't yet have the check you mentioned. But it is indeed the file does not exists warning.
But then again, why run code on file's that aren't PDF's anyway ?

8.x-1.2 is out and includes the fix mentioned in #3.