This all assumes the idea of the project having both a huge body of skilled and experienced soldiers and a huge body of high quality, hi tech military gear.
I'm not sure that was ever the case. In Desert Search they point out the project didn't even have night vision for its TOW launchers. MARS teams rarely seem to be more than 3 or so vehicles and maybe 20 people.
This is suggesting that once you include support and maintenance staff the Project had something like 10% of its MARS teams just defending Prime base. That's before you even get into the space required for garaging the vehicles, bunkering the troops and storing the ammo.
Even then assuming the threat level the project was up against; Warsaw Pact invaders, rogue battalions of the army, thousands of refugees then even a couple of dozen light armoured vehicles wouldn't have made much difference.
This might be enough to defend an airfield in a war zone, but even then that's assuming you've got a lot of cavalries to come over the hill if really needed.
More likely I'm guessing Prime's security would rely on the following.
1 Not being seen the Project got pretty good at hiding its resources.
2 Automated defences, again the various scenarios suggest a preference for robotic style gun emplacements, smart mine fields etc.
3 A completely separate security force and the kicker is probably not knowing what they were defending.
The project seemed to have great strengths in both ruthlesness and secrecy in a noble aim.
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