A recent voice actor on the show has said production on the show has stopped.
Source: Episode 54 Guests: Jason Marsden
During an interview on the Talking Toons with Rob Paulsen (yes the voice actor who's currently playing Donatello in the new TMNT series) podcast, Jason Marsden, the voice of Bart Allen/Impulse on Young Justice revealed some bad news. Around 1:12:00 into the interview Paulsen asked him if he be returning to the show for a Season 3 to reprise his role as Bart Allen/Impulse, Marsden responded:
"They finished production right now. They do half seasons. Season 1.0 where they introduced my character. Then there's another half season and that's going to be it."
This has been the second bag of evidence that the show won't be returning for another season. Not just a two months ago, Mattel had canceled the final action figures for their Young Justice toy line, which was clearanced off toy shelves of stores earlier this year.
As for reasons why? By the end of season two, the show will have well close to fifty episodes. That's the usual amount cartoons of it's kind have nowadays. The other reason? Well, two new DC shows will be hitting the waves next year in Beware the Batman and Teen Titans Go!. With only an hour block, the DC Nation is crammed already as it is.
However this should be noted this is still speculation on the matter. Warners Brothers or DC haven't fully confirmed that the current season of Young Justice will be it's last. Not to mention we're still barely into it's second season as it hits it's tenth episode this Saturday.