Because they're protected by the ship's shields. As I said before, these should be able to deflect focused electromagnetism in the same way they are able to deflect focused light or radiation.
You say "obviously didn't require much effort" but the text in your scan says "Magneto struggles desperately to minimize the force of the nuclear reactions--" The expression on Magneto's face and the way the muscles are standing out in his neck also demonstrate how difficult this is for him.
Technically, there are "multiple" missiles, though your scan shows that multiple means "two" in this instance. They are US missiles and the most powerful warhead currently in the US nuclear arsenal is the B-83, which delivers a yield of 1.2 megatons. Therefore, based on your scan, Magneto is at his limit containing a combined release of 2.4 megatons. That's very impressive, but a single photon torpedo (and thanks for providing this info) can deliver about 30 times that much energy.
You haven't answered the objection I've raised twice about the level of energy. Your scan shows that Magneto can affect light-based attacks but this does support your assertion that he "literally has all control of it." To be able to gain control of any light based attack regardless of how powerful it is would require him to be infinitely powerful. You haven't provided any evidence of that.
He can overcome Dazzler's attack because he's much more powerful than Dazzler. I'm sure he could handle hand phasers pretty easily too. But Dazzler's powers are puny compared to the Enterprise's main phaser banks. As your scan establishes, Magneto's upper limit is alightly better than 2.4 megatons (which converts to 10,000 terajoules) of energy. The ship's main phaser banks have comparable power to her photon torpedoes and will generate about 30 times what he can handle.
To go back to your question "why doesn't he just crumple the ship" it's because he can't, he's not powerful enough.
In "Into Darkness" the Enterprise survives multiple phaser and photon torpedo hits. We know that any of these hits is equivalent to a 60 megaton nuclear explosion, which should obliterate a vessel of her size. Instead, they do very localized damage. This is because the ship is held together by structural integrity fields (they are needed to withstand the acceleration stress of warp speed and even the accelerations at sublight speeds which would tear any metal ship apart.) They make the hull of the Enterprise so durable that these powerful weapons only do the damage you'd expect from big conventional weapons, like battleship guns. The 10,000 or so terajoule Magneto can muster may cause some very minor damage but its far short of what the Enterprise can take.
So, the encounter probably goes like this: Sensors pick up a man flying through space. Kirk orders Uhuru to hail him. Magneto is non-responsive and keeps coming. He tries to crumple the ship with his powers but the structural integrity fields are too much for him.
Kirk, not wanting to risk minor damage has the shields raised. Magneto finds he can no longer affect the ship directly and begins trying to breach the shields. Spock says that there is no immediate danger but, if he is able to keep up this level of attack indefinitely, he may eventually get through. Kirk orders a phaser burst on 1/20 power which overloads Magneto's shields and renders him unconcious (if he's lucky.) He can figure out what to do with him at that point.
The problem would be if Magneto managed to get on board. I don't think there's any way the crew could deal with him if that happened.
First of all, the strongest nuclear weapon in the United States arsenal is the B41 with a yield of 25 Megatons. Second of all, those nukes were SPECIFICALLY designed to take out Magneto (which is why they exploded when he tried to deflect them), which means they could easily be of a higher output to ensure Magneto is dead. Second of all, like I've said three times now, he was before literally trying to manipulate the magnetic field of the entire planet, putting him in extreme pain, and then he got nuked completely unexpectedly. Also, directly afterwards, he fought Joseph (a being more powerful than himself) and the entire X-Men. So obviously, fending off the nukes didn't keep him down for much time at all.
Not really. If he has "absolute control" of the entire E/M spectrum he can deflect all electromagnetism. There has been no indication that there is a limit to this ability, or that it depends on the energy of the light. In any case, in Silent Enemy (Star Trek: Enterprise) the phase cannons had a maximum output of 500 gigajoules, which Magneto can deflect rather easily, and that's assuming that they would full out attempt to annihilate the f*ck out of what appears to be a dude floating in space (extremely uncharacteristic of the Enterprise I believe).
Are you sure it was the hull only and not the deflector shields? Because I don't think deflector shields can deflect what appears to be localized magnetic fields, which can be created inside of the shield or even inside the ship (he can also create electric fields inside the ship, meaning all non-shielded consoles and such are toast).
Even if it was, the structural integrity fields at their max can take 82 * 10^9 Dynes (TNG: The Loss) (why Star Trek uses made up units, I don't know), which is equivalent to 820,000 N (1 dyne = 10^-5 N). Using your figure for 2 million tons as the weight of asteroid M, Magneto can easily override the structural integrity fields of the Enterprise with little to no effort whatsoever.
Also, you never countered my point that what if Magneto deflected the missile right after it exited the Enterprise?