That is correct ... files uploaded to moodle do go to moodledata/filedir/ ... but not by humanly recognizable filenames.
When you upgraded from 2.x to 3.x did Bitnami allow you to upgrade just the code or did you have to re-install bitnami - the php, the apache, the mysql DB included. Did you make a backup of the site before upgrading? How about ownerships/permissions on moodledata?
Looks like Bitnami has docs on moodle upgrades:
Their docs may not mention that one should check the environment in moodle to see if one has correct versions of php and mysql.
Anyhoo, because Bitnami is 'different', you best resource ... 1st resource ... are Bitnami forums and docs.
Any advice you get for free here in these forums or docs you might find probably have to be translated to 'Bitnamese'.
'spirit of sharing', Ken