What kind of damage would low-level supersonic flight inflict?
The video is highly inaccurate in that area.

The actual damage the missile would have caused would have been largely radiological, from ejected radioactive material in its exhaust plume.

While windows and weak structures may receive damage from extremely low flying Mach 3 bodies, this would probably be limited to say some broken glass.

The plan was also never really considered. What was considered is having the weapon, now without its warheads, fly to a final target area and do a high speed dive into the ground, the kinetic energy alone combined with the spread of radioactive material from the rupturing nuclear reactor causing the damage there.

Mind that the damage (both physical and radiological) of the weapon flying overhead isn't clear. Different sources list different predictions.
Some way the damage would be minor, others that it would be severe. 
But rest assured, the noise would shatter eardrums, the supersonic shockwave flatten crops and lightly constructed buildings, and the radioactive exhaust plume wouldn't have been healthy either.

I've always found this to be an excellent article on the project and the people surrounding it.

Edit: a very interesting article by the designer of the reactor about the problems inherent in the reactor design, and how he thought about the radiation hazard for people on the ground working with the missile:
Merkle public paper