While the military arms at the time were muskets and bayonets, that was not the only technology available. Many colonial troops had rifles of their own that they used. These rifles were superior to the British musket in many regards and helped the colonial troops win.

Surely the founding fathers were aware of this and knew that the second amendment would allow citizens to have weapons that were more deadly than the standard military firearm at the time. In fact, this trend even continued well into the Vietnam war. It was really only in the past 50 or so years that the military has eclipsed the citizens in terms of standard issue firepower.

So no, the founding fathers were not aware of the M-16 and AK-47[0], but they also had more than muskets and bayonets, and were perfectly content to have a citizenry that outgunned the military.

[0] - I should note that the M-16 and AK-47 are essentially illegal in the US at this point, along with any weapons of similar firepower, so that point seems moot anyway. The only people able to acquire them are incredibly rich collectors.