Recover Smart Mailbox

Try re-indexing the mailboxes. This can take awhile if you have a lot of mail.

Reindex messages For El Capitan, try looking in V3. Sierra use V4. High Sierra use V5.

Reindex messages (2) See post by Linc Davis

Once you delete the apple mail account by going to system preferences > internet accounts and subtracting the account it is deleted from Mac but the data ( for sent and inbox mails are stored on their servers ) .

The V4 folder in user library is storing them , as mentioned you can not create smart mail boxes on the server end and there is no feature to add them or download them in apple mail application .

You create a smart mail box in your Mac and in case if you delete from on my Mac section it will get " removed " .

Also you wrote - What I am hoping is that my deleted email account and all its messages are being stored somewhere in the depths of my laptop, just not somewhere that is readily accessible.

You can click on V4 folder and view alfa numeric folders where the data for inbox , sent , archive , deleted messages is stored .

Smart mail boxes are created by Mac user in apple mail application under on my Mac section , they are clones of all mails in inbox / sent folders of the web mail account .

You can not create a smart mail box on a web server , even you delete the IMAP account , use rebuild / reindex method or even create a new user account .If you right click on smart mail box and delete it , it will never influence your mail data .

Read this article Use Smart Mailboxes to organize emails in Mail on Mac - Apple Support

See an example screen shot .

You are welcome. Do you have a backup you can restore from? Are the e-mails on the e-mail provider's web site?