SQL query to identify missing hinted indexes
Personally, I would start with DBA_HIST_ACTIVE_SESS_HISTORY, and look at all statments that contain that type of hint. 

From there, you can pull the index name coming from that hint, and then do a lookup on dba_indexes to see if the index exists, is valid, etc. 

You should be able to do this via PL/SQL if you want to make it really fancy and do it all in one step, otherwise a few pieces of SQL and a spreadsheet application can be your friend.