Let's put it this way, it's the only illegal drug you could have done and still be eligible. If you did crack, heroin, ecstasy, you're done. That's what my recruiter said. He then said, if you've smoked pot, it's ok, just tell me now, and basically promise not to do it again.
It shouldn't affect your chances. One of our guys at OCS for Sub nuke smoked pot before, and he got the necessary clearance to be a nuke. I think the navy realizes that people are going to experiment.