When a user is finally removed from Azure AD, their profile gets updated in SharePoint as "Deleted" and is then moved from Active Profiles to "Profiles Missing from Import." Is it necessary to manually remove these or will they eventually drop off as well? And if they don't automatically drop off, is there a good PS script that can query this? I've been looking but coming up short.
I would suggest you manually remove the deleted users from SharePoint Online since their profiles can be kept in sites for a very long time.
You can refer to the link below for a sample PowerShell script to find and delete orphaned users:
Another document that might be useful: Remove a former employee.