Once you are IN the military it will kill your career, and they are very upfront about that so you really can't complain that you weren't warned.

If it was recent, you're toast unless you are young enough to wait a few years. However a DUI (or even light drug use) in your distant past may not disqualify you from getting a commission and a flying slot. It likely puts you at a competetive disadvantage, but it may not be disqualifying...the policies and competetive realties flucuate with supply and demand, so only a pilot recruiter could give you a straight answer (NOT the enlisted recruiter at the strip mall...he'll tell you that you can't be an officer or a pilot but he can get you a job fixing truck engines )