Per update-desktop-database(1), the database is only a cache of MIME types handled by desktop files. Therefore, updating it is only necessary if .desktop files specify MimeType=. However, the eclass updates them based on mere presence of .desktop files which is wrong.
Given that the eclass does not check the content of the files at all, it is probably better to call update-desktop-database than not. Checking the file content before calling it would be an enhancement, not a bug fix.