Did you set up the account with POP3 or IMAP?
The default for @hotmail accounts in Aqua is IMAP -- which should reflect messages being moved, deleted, marked read / unread, etc.
But if you used Manual account setup and chose POP3 -- this protocol is much more modest (from 1996). No folders, no read/unread sync, and messages won't be deleted from the server until you empty the Deleted folder in Aqua.