Do I need to run the newMM.pl script every time I self certify a device
No, you do not need to run the NewMM.pl script after self certifying a device.
Typically you would be running the NewMM.pl script after an upgrade when there may be changes to models, new models introduced.
If a device you had self certified was to then become at a later date certified Out Of Box in a later version, that you then upgrade to, you would in this scenario run the newMM.pl after upgrading.
This would be to convert the models created when self certifying to the new model that is now certified Out Of Box.