Can the court in anyway have access to a deactivated Facebook account? And if so, can they recover the permanently deleted account?
@dnbrv said it right that a court can subpoena the data that Facebook would have about the account. Especially the part about knowingly deleting the information if the subject knows he/she is under investigation.
But beyond that, you are asking specifically about a deactivated Facebook account. For those account types the information isn't ever deleted. It's just not displayed on the site anymore (although links to images are likely to still be in existence just not displayed in albums).
Your second question:
And if so, can they recover the permanently deleted account?
This is a little misleading.
Deactivated accounts aren't deleted, as I've stated above. You can find more information about the difference between Deactivating & Deleting your accounts at Facebook's Help Page: Privacy: Deactivating, Deleting, and Memorializing Accounts