If the video is MVC, then it will be decoded at full resolution (e.g. 1080p for each eye).
If “Use Full HD HDMI modes for 3D” is enabled then the video will be output at full resolution. If it is disabled then either half-SBS or half_TAB will be used for the video.
Note: for MVC with “Use Full HD HDMI modes for 3D” enabled, the SBS/TAB settings only affects how the GUI is rendered - the video will identical (and full resolution) in both cases.