-user left company 3 months ago
-E3 licenses was removed 3 months ago
-mailbox was on litigation hold while user is still active
if we are about recover her mailbox data, will data still be available even if user was already deleted in O365 tenant?
Did you delete the user while he was still on hold? If so, the mailbox will be provisioned as Inactive mailbox and you can still recover data from it: https://docs.microsoft.com/en-us/office365/securitycompliance/restore-an-inactive-mailbox
If there was no hold, the data is most likely unrecoverable.