I've started thinking on a Traveller setting that takes all the Traveller assumptions and turns them on their head. So I get to this one, and I want it not to be the undiscussed elephant in the room.
I think, in my ATU, this will be a thing. People -- terrorists mostly -- do occasionally try to crash ships into planets at relativistic speeds.
Governments don't do it that often, because of mutually-assured destruction pacts, nobility / fiefdom repercussions, and so on.
But it happens. To prevent it, you need a defense network light-minutes away from your planet. You need beam weapons that can obliterate (and, ideally, redirect) any mass with a threatening vector. You need a pretty harsh policy about ships that are even starting to look threatening: this suggests that if you want to land on a planet, you follow strict protocols to avoid even the appearance of threatening acceleration, or you wake up the mesons.
My ATU is a sundiver / sungate (wormhole) universe with no true FTL, but high-G M-drives are a thing. However, incoming ships will be coming from the star, not coming from the outer planets. Doesn't mean there aren't ships out in the far bands for mining and stuff, and those are carefully watched.
I suspect the nobles also will carefully control who gets a starship. It's essentially a planet buster, so not you can't just let everyone have one.
IIRC your ATU is described in
this thread. If so, as you decribed it, ships travel by hack drive at about 0.1 (or 0.01, as you fixed latter) speed, not by acceleration. So, unles you changed this (after all it's YTU), this would not be a problem.
This aside, and still keeping IYTU, the fact the sungates are always in the sun (or close to it) makes a good defense against that. Planetary ship must only patrol the sun-planet straight line, as it wil lbe the only one travelled by intesrtellar ships (and I guess interplanetary ones are monitored by the local government), and any ship straying from this route without a good reason will be seen as hostile. Similarly, if using acceleration, any ship not turning at midpoint for deceleration will also be seen as hostile.
As for stopping them, their own speed is the best weapon against them. Just throw some rocks on their way, and they will be obliterated (though, as you say, this must be done far from the target). See that if the ship is going at 0.5 C, throwing some rocks (let's say, a shotgun like spraying rocks group of 1 kg rocks); and those rocks will be hiting it at 0.5 C (relative) speed. You can run the numbers if you want, but just let's say no ship will survive that, and if its speed or agle is affected (even very slightly) it is likely to miss the planet (the farther you can intercept it, the more likely it will be to miss if its vector is afected).
Strategically, and not entering in detail (as it would be Pit matter) most terrorist groups have a political claim behind them, and their goal is to gain supporters, as much as creating fear. Such a move will make them quite unpopular even among their sympathyzers (unless blind fanatics), and probably backfire politically.
