Blu-Ray.com called attention to an SCEI press release about the features of the new Blu-Ray 3D function for the PS3 (info also available in English here). It specifically noted that when playing a movie in 3D, audio will play in DTS or Dolby Digital when your system is set to output DTS-HD or Dolby TrueHD, respectively.

Blu-Ray.com's Joshua Wingfield tested the 3D playback: "I can confirm that with the PS3 3.50 firmware update it only puts the audio out as DTS standard (lossy) in the bitstream mode. Also the menus on Coraline are flattened to 2D. Subtitles still show up in 3D mode, and so do menus. The image just flattens." Note that he didn't seem too put off by the limitation, saying, "So for now 3D on the PS3...full 1080p to each eye, but no HD audio and no 3D on menu screens or pop up menus. Can't say I'm disappointed."

The PS3's 3D capabilities remain impressive, though not quite perfect. For 3D games, you have to lose some graphical complexity (in order to render two images simultaneously) and for 3D movies, you may have to sacrifice sound quality. And you sacrifice some of your time learning about audio codecs.
Source- blu-ray.com