Using the New Outlook for Mac for personal email and calendar
Since junk mail still reaches you, your account is receiving mail, so the missing messages are being filtered or moved somewhere instead of landing in the inbox.
Sign in to your mail at outlook.com in a browser and check there. Look under the Other tab if you use Focused Inbox, and also check the Archive, Deleted items and any custom folders.
Then open Settings, then Mail, then Rules, and delete any rule you do not recognise. A stray inbox rule is the most common reason normal mail disappears while junk still arrives.
If the messages show up on the web but not in the Mac or iPhone apps, remove the account from those apps and add it again to force a fresh sync.