Why the nexus and arks were not armed (theory)

Disclaimer: i get the fact that the writing for MEA was very week and was incredibly weak on lore. So no need to jut say its bad writing we are all aware of that, just humor me. 

It is well known that one of the many mysteries of the the AI is that why did the arks or the nexus have no on board weapons or counter defensive measures. They barely have enough small arms to hold back a boarding party (which i think the only time a boarding party was actually repelled was on the Asari ark.) let alone to hold back any war ships. Now the AI was a quintillion credit program and the benefactors main reason to fund the program was to save milky way civilization. So why dedicate so many credits to leave out such a huge oversight as not arming these vessels just in case. Granted we see these ships are decently built, but they are far from invulnerable. Like we see the arks have run in with the scourge and take beatings from kett ships and still make FTL jumps. But we see with a turian ark though the hull was mostly intact-ish, we see the ship was mostly if not completely disabled with most hands lost. And even the asari arc was heavily damaged to the point of almost being disabled. So why the oversight? they were civilian ships true but didnt stop the AI from violating intergalactic law with using A.I., and also bring on former terrorists, mercenaries, and criminals so AI was defiantly not against breaking the law. And as far as im aware of there is no law in the ME universe that says civilian ships cant be armed with on board ship weapons or counter measures. And what is stopping them from at least adding a ton of armor to the ship to tank the damage.  

So my theory: they were originally designed to have armor and on board weapons. This is to large of an oversight to ignore. But they were canned later in production of the Ark and nexus because of the fact after the Geth and sovereign attack we know Alec just the time table to launch within two years. As he already have the capital, he canned the on board weapons and armor to speed up the construction of the arks and nexus to get them out on time. This decision costed at minimum 2 arks and tens of thousands of lives.

What do yall think? Will more come to light with the new booK?