Workaround (at least this works in Cubase 5)
If you setup a mono output next to you stereo Main output
Route your stereo tracks to the stereo out and your mono tracks to the mono out, you can then use the batch export and all stereo tracks will be stereo and all mono tracks will be mono.
So the only extra work (though granted it should not be necessary) is rerouting (Select all mono tracks the SHIFT select you output, all will be don at once) your tracks, and after the batch export routing them back again).
Peter