What would the effect of ablative armor in the missiles be? ...
Trivial. The ship's laser's supposed to be able to punch through ship armor, which starts at equivalent to a foot of steel. That's close to two inches of bonded superdense armor on a missile that's supposed to come in at 50 kg with fuel, warhead and guidance. It isn't carrying armor, and any conceivable ablative coat that would be as effective without impairing the missile would also be a dandy armor for a ship, even if it were only good for a few hits.
...I assume the missiles to take evasive moves while in movement to their target. If so, the probablility to be hit while pointing the arget is quite remote, so one hit is one miss for them. And remember odds are the arget is also evading at very high speeds...
First, at terminal stage there is no evading: the delay between the missile image reaching the sensor and the laser reaching the missile is measured in milliseconds, even at ranges of a few hundred kilometers. The missile dives in and "hopes" for the best because nothing short of an instant teleport device is going to save it if the laser is on target.
Second, you're looking at missiles closing at velocities in the tens of kilometers per second and suggesting that a lateral thrust of less than a meter per second is going to significantly alter its impact point. Maybe if it's a few hundred klicks out with several seconds yet before impact, but not if it's only a second from impact.
At 6G, a ship can displace itself 30 meters in a second. Assuming the missile is reasonably on target before it's killed and that it's killed one second out, the craft able to move out from under in that time are the boats and the smaller ships, roughly a thousand dTons and under. Given, say, five seconds, the ship can displace itself 750 meters - which is enough to save even a dreadnought.
... Ships lasers retain high probabilities of hit for hundreds of kilometers.
And that's my thought: the lasers are killing the missiles, or trying to, at ranges of hundreds of kilometers. If they can hit ships at light-second ranges, they can hit missiles at a thousandth of that range. If you wait till you're guaranteed to hit, he is too. (On the other hand, I would still expect better laser accuracy than we're getting.)
In any case, as MT is depicted (and as tables are shown), I'd expect most of orbital pinpoint fire to be conducted by beam weapons (lasers and energy weapons, PA may also help if there's no atmosphere and if you want their nuke-like effect), while the missiles only used for area fire (mostly against dispersed infantry, too numerous to be taken off by pinpoint fire), ...
Why? Missiles as portrayed in Striker are quite effective. They drop from orbit and then home in on a detected target, better than a laser-guided bomb since they have their own guidance and their own drives to pursue the target. Odds of a hit are quite a bit better than by indirect fire rules using orbital beam weapons. Only drawback is point defenses, and enough missiles will overwhelm that. Since MT draws heavily on Striker, I'd expect similar behavior.
...Those beams are quite lethal and precise in atmosphere, do not use ammo (if you're attacking a hostile planet cargo space would be at a premium), and are more difficult to stop by PD weapons, so I expect them (and fighters) to be the main ortillery weapons, instead of missiles.
Ship lasers and energy weapons in MT have a range attenuation of 5, which means they're full penetration to 500 meters in atmosphere, half pen from that point to 50,000 km. Effectively, they're half pen when fired from orbit at targets on the battlefield. MT did away with that armor face business that Striker had, so for example a TL13 beam laser fired from orbit, hitting a Zhodani Z-80 tank matches its penetration of 37 against an armor of 40 - it doesn't penetrate. Useful against thinner-skinned vehicles and troops, of course.
Pulse lasers and energy weapons have good punch and a decent danger space, but penetration declines quickly away from point of impact: half at 1.5 meters, quarter at 3, one eight at 4.5 and so forth. Outside of 3 meters, they won't penetrate TL14 combat armor. Outside of 4.5 meters, they won't penetrate the TL12 stuff. Something with an armor rating of 52 will withstand a fusion-15 fired from orbit.
Despite being straight-line weapons, orbital beam artillery must still use indirect fire rules. Someone has to spot for them. Indirect fire is a difficult task (11+ on 2D6 to hit the target zone) with a bonus for Forward Observer skill. I'm not sure what the role is for those in the area to be hit if you hit the right area. It's also "fateful": a mishap is guaranteed if the task fails. I am ambivalent about that rule. Not every miss in indirect fire results in a friendly fire incident.