When I do a search for an email in Apple Mail it'll typically show 2 results for each search. 1 in 'All Mail' and 1 in 'Inbox'.
Is there a difference between the 2? Is it essentially taking up TWICE the hard drive space?
The 'all mailboxes' indicates you're SEARCHING all mailboxes, not necessarily that there are multiple copies of a message. If you only have one inbox, then 'all mailboxes' is the same as 'inbox.'
If you have multiple mailboxes, here's where the distinction becomes helpful:
In my case, I have 4 email accounts, plus extra 'on my Mac' mailboxes that I've created on my sidebar. If I know that the message I seek is on my .mac account, I can choose to search only the 'Inbox' and speed up the search considerably.
If, on the other hand, I don't remember when or where the message came in, I can have it search 'All Mailboxes' and the system will look through all mailboxes from all accounts.
In your case, even if you only have one inbox, searching 'All Mailboxes' can still help, because it also searches the trash folder and junk folder (each appear as just another mailbox to the system).
Hope this helps!