It is possible to resize the GPS window during any flight session. However, it will resume to its default value once FSX is terminated.

To make the change permanent:

1. Open the panel.cfg of the aircraft to be changed
2. Locate [Window02] section
3. Decrease the value of window_size for smaller window (0.4 or 0.35 represents 80% or 70% of the original size), or
4. Increase the value of window_size for larger window

Note that there isn’t any shortcut that could altogether resize the GPS windows for all aircrafts simultaneoulsy.  It can only be changed one by one as described above.