I have the same issue over here after a clean install of Yosemite 10.10.2 and restore from time machine. Note that i could not restore my accounts with the Time Machine, but I had to manually copy my accounts to the mail app out of the time machine backup.
I've already had issues in the past where searching didn't always show the result i expected (being sure that there were mails meeting my search requests).
Now I cannot : search in mail (always 0 found), smart mailboxes stay empty, even new smart mailboxes.
Spotlight shows however good results in my mail search... (although order is very strange)
I've tried everything from reindexing with spotlight (even with terminal command), cleaning index file in mail library, correcting settings in my mail accounts (which have been changed by yosemite),...