Whirligig supports external srt files that are placed over the video rather than as part of the video so 3D content will work. This is not true if you choose to use muxed subtitles though as the 3D will screw them up.
Viewing post in Whirligig VR Media Player comments
It works! After trying (and buying) a few media apps the subtitles work. They display at only one point but I think making them show up where your looking is a deceptively complex problem to solve.
The interface takes a bit of time to get used to, but it's incredibly powerful once you understand it. with the amount of custom formats and ways to tweak output I bet there's no 3D video this thing won't play.
Thanks you very much!