Yes, it can shutdown your system via its relay or the aquasuite software. At least you should get the relay plug to connect the aquaero parallel to the power button of your case so it can "push" the button to shutdown the system. Also this can be configurated in detail - a few seconds to make sure that the system switchs off or only one second to act like you would go into standby or whatever.
You can also use an ATX adapter to directly switch off the PSU.
http://www.shoggy.de/ac_forum/ae_pwr_taster.png
To monitor the pump you will need a flow sensor or a tacho signal from the pump or an aquastream ;) Or you combine all of them :D
edit: Brodholm, you can
download the aquasuite and start it in a demo mode. Maybe then you will get a better idea of the possibilities.