The MessageQ limit is set due to possible memory constraints in SharedRegion when creating a significant amount of MessageQ. A typical application only uses a few MessageQ to communicate between cores.
If you want to make changes to the default HLOS configuration take a look at:
http://processors.wiki.ti.com/index.php/SysLink_UserGuide#Configuration
In the MessageQ runtime entries max (default 32), you must ensure that both your BIOS-side application configuration (*.cfg) and the HLOS-side agree.