Are you using an IMAP server?
Try right-clicking on the top level of your email account, i.e. the name of the account, not the Inbox bit. Then choose Subscribe. A menu should load. If you expand the Inbox you should be able to see the Junk folder. It probably hasn't been ticked in the corresponding box. Tick the box for Junk/Junk Mail or whatever it is called. Then click Subscribe then OK. You should be able to see the Junk folder. If not restart Thunderbird and it should be there.