Hypack does indeed work with G-880, G-881 and G-882 magnetometers. A number of survey companies use Hypack as the primary recording device for Geometrics magnetometers. 
The Hypack driver does not transmit configuration commands to the magnetometer. If you are purchasing an instrument, it is a simple matter for us to provide the instrument with a custom default configuration that will match your normal survey requirements with Hypack. If you already have a magnetometer with a standard configuration, you will need to transmit commands to enable optional depth and altimeter outputs and possibly to change the measurement rate. This is easy to accomplish with the Utility software available from our web site, http://www.geometrics.com/geometrics-products/geometrics-magnetometers/download-magnetometer-software/  We ship a copy of this software with each Cesium Marine Magnetometer.

An alternative to recording the magnetometer with Hypack is to use Geometrics MagLog Lite recording software. MagLog is designed to provide a flexible automatic recording environment. It includes Survey Wizard that can automatically find the appropriate serial port and baud rate for both the magnetometer and position inputs. MagLog automatically sends configuration commands to the instrument. MagLog requires a Windows OS computer. It has been successfully operated on surveys with Hypack navigation systems by several survey companies