If the Second Amendment (2A) meant to preserve the ability to overthrow the government then why can we not have bombs and tanks?

And why does it mention the right within the context of a "well regulated militia"?

Could it be they feared having a permanent national army, so did the 2A instead? Only later to realize having a standing army were necessary after all?

No that couldn't be it. Because then there would be no rational reason for keeping 2A and flooding the country with deadly weapons.