I suspect it isn't a proper POP3 account, which would retrieve all incoming mail including spam, but retrieval by POP3 of messages in the Inbox of a web-based service. Messages which have been filtered out from the Inbox won't, as you've discovered, be downloaded.
IMAP will replicate all of the folders on the server in each of the computers with which it is set up.
What your wife could do initially, to safeguard her saved business mail, is to set up Apple Mail with IMAP to see exactly what is there that needs to be retained. If all her business messages are still there on the server, she could then change Outlook to IMAP too, but would have to set up her various existing folders on the IMAP server.