Using AAC-HE for 5.1 audio?
What are the limitations of AAC-HE codec while doing 5.1 audio ?
  


HE-AAC v2 can only encode stereo from my experience with Nero AAC and the article in Wikipedia about Parametric Stereo.


  
  Why is AC3 preferred when compared to AAC-HE ?
  


Which case are you actually talking about? Are you sure it's HE-AAC not AAC-LC? Dolby Digital / A/52 / AC-3 was the standard for video DVDs which makes it the most common digital audio format for video. It achieves acceptable quality at significantly less bitrates than the competitor DTS and newer formats developed for video on physical media. AAC-LC is usually offered for official downloads and streaming and is part of the MPEG4 specification.

To add some perspective, HE-AAC was one of the early efforts to develop a codec suitable for low bitrates providing high quality audio compared to earlier speech only audio codecs. Opus is a successor with many improvements in this field and which also offers multichannel capability. Some podcasts offer it as an additional option to Vorbis. It's part of later WebM revisions and can be decoded on recent Android devices but its adoption seems to be very slow. If you are looking for a solution to high quality multichannel audio at low bitrates you should be looking into the state of the art Opus, not old AAC with extentions.

The general recommendation has been to use AAC-LC and to avoid HE features which may cause playback issues on some devices.