First a note about Henrik's problem above, we found that this was a problem relating to the length of the messages that were being sent between the programs (highlighted when many other ships were loaded), and this has been resolved in version 5.6 and later.
For the AIS query, Bridge Command (via the Map Controller) can currently read real AIS data so you can have real world, real time ship movements in a scenario. However it does not currently generate virtual AIS data for the ships in the scenario. I can look into this, but in the mean time, the closest thing is that if you have ARPA enabled on the radar, it will send out the NMEA 'TTM' message (tracked target message) for each tracked target. To receive this, configure the NMEA settings in the normal way, and it should be visible in your chart plotter.