Snyder had to say "I don't know for sure, I can't say for sure but I will say that the experience of the 3D in Guardians was so successful for what I wanted it to do. I think that 3D is pretty awesome if it's done as part of the cinematic language as opposed to being a gimmick."
Even his Wife Deborah Snyder said she wasn’t for sure about if it will be shot in 3d or not Stating "really just too early to tell" But her excitement about working with Christopher Nolan and Emma Thomas has been growing since her and Zack signed on saying "We have such enormous respect for Chris and Emma and their work," she said. "We've been such fans and we're just thrilled to be working with them."
When talking about Donner’s version Snyder remarked "I like the Donner version. It's hard not to like it, it's so awesome but I don't think this will have anything to do with any of those."
To Point out Bryan Singers version of Superman, it did in fact have a 3D conversion on certain scenes exclusively for IMAM theaters.
With all of the 3d conversion techniques and attention to detail Zack Snyder has it should be noted that The Superman Snyderboot isn’t due out till 2012 so chances are Superman may very well have scenes shot in 3D, Superman is to huge of an iconic character not to be released in 3d.