After changing oil and getting very close, I could see some rust and shedding metal.

How bad is this and what can I do?

Trivial, ignore it.

Is there a subframe bolt missing in images 1, 3 & 4?

I'd be inclined to wire brush it, treat it with a rust converter and paint it, or Waxoyl it.

1 hour ago, Warrior193 said:

Is there a subframe bolt missing in images 1, 3 & 4?

I think not, those are the ones that hold the tray under the engine that I took off for oil change

I would also wire brush the flaking metal and use a proprietary rust converter like FERTAN, primes and then spray with chassis black.

If you live near the coast you need to keep on top of it; a neighbour bought a Honda Civic from someone in Brighton that on the face of it looked nice. Wasn't till he had it MOT'd that he found it was rotten underneath.