Apple Mail, how do I hide the Archive folder?
So here's kind of crappy workaround, but as for me it worth it. The solution requires one external useless email, say useless@mail.com, maybe fresh generated or some old one. 

Starting settings: You have several mail boxes that is shown in Archive parent mail box. So the Archive box shows as extendable one, e.g. with the arrow that allows to expand it to see included mail boxes.


In some useful mail account, say useful@mail.com, in the web interface create some additional folder, like "arch" make sure that it available by imap.
In the "System Settings" -> "Internet Accounts" add some additional useless email account.
Check that it shows in mail.app
In the Mail "Preferences" -> Accounts -> useful@mail.com choose "arch folder as the Archive one.
In that point you're should have extendable Archive folder in mail.app (like any other Folder which have subfolders).
Expand Archive folder to see what subfolders it have.
Select the one that are from useful account, hit right click and select "delete mail box". 
After mail.app have been reload its state you should have non extendable Archive folder again. (If this is not true — make steps above till it will be). And the only one mail box in it is the useless one.
Completely delete useless mail account from system.
Restart mail.app and there's none Archive folder.