Who makes the to hit roll for a cruise missile? The computer that programmed its route, the onboard computer that responds to environmental changes, or the targetting sub-routine on final approach?
Ultimately it will depend on the specific scenario since there are a lot of variables to consider. It also depends of you are using smart missiles, intelligent missiles fired from a weapon equipped with a smart tracker or actual "robot" missiles since the game rules are different. It depends if your "cruise missile" is a ship to ship missile (as the space combat rules blur a lot of the nuances for a ground based missile from CSC or the Field Catalog). You could create a custom cruise missile from using the Robot Handbook and then you would need to come up with your own rules since investing significant effort into highly capable targeting and sensor packages should provide some benefit, but there doesn't appear to be scope for that in the core rules.
It depends on if it is dumb missile, or has a drone interface or robot brain. If a dumb missile it is the computer or gunner that programmed its route, once it is launched it cannot respond to any countermeasures (but space combat takes no account of the gunner skill or range). If it has a brain it will use its own terminal guidance targeting, but if it has a drone interface it could also be overridden by the mothership if that has a better targeting solution.
It is complicated as the default missile in Traveller are not specified as being drones or robots (but are Smart - which itself means different things in different books). Thus the normal rules for missiles that have drone controllers or brains should be different from the default weapons. For example they may be immune to ordinary ECM measures (or at least require a contest of skills between the ECM and whatever is guiding the Robot/Drone missile.
The effectiveness of mothership derived targeting information should be subject to range modifiers at the range of the target from the mothership, the missiles on-board systems will be at the range of the missile when it implements its terminal guidance routine (at short range proably). Even a primitive brain taking no range modifiers can have more chance of hitting than a more sophisticated system that is at long range, but as stated space combat with missiles ignores range.
A cruise missile will tend to have at least a Primitive(homing) brain which is good enough for the large targets (or GPS coordinates) it is usually designed to defeat. On launch the target will be designated and unless that designated target disappears from its sensors (which may require Recon checks if the target is evading or jamming effectively) it will pootle over to it and whack it out. If the target is a friendly then it will be for the mothership to abort since the primitive brain has no IFF capability (lets hope it has a drone interface).
Larger weapons might have more sophisticated brains, which should have anti-jam capability and probably some point defence evasion capability, but large targets are quiet easy to hit and rely more on shooting down or breaking sensor lock of the incoming missile than dodging making really smart brains on comparatively cheap missiles uneconomical since you might need to launch many to overwhelm any point defence capability. You might be better off launching a drone missile carrier to close down the range and then launch a salvo of less sophisticated and cheaper missiles from it which can manage the terminal guidance (like a MIRV). You might even be able to recover the carrier after the engagement, but even if not it will still probably be cheaper that having multiple missiles of equivalent sophistication.
Standard ship missiles are around KCr21 each which is a little cheaper than the KCr24 one in the Robot Handbook that has a Primitive(Homing Brain). Now we could put that down to a bulk discount for buying them by the dozen. If so we could make a ruling that this is basic missile and with a Primitive(Homing) brain it has no counter-ECM capability. It should also be noted that the to hit roll explicitly excludes the range or any gunnery skill (and doesn't mention Remote Ops). Perhaps even with this interpretation of the standard ship smart missile a Remote Ops could be used with the drone interface to provide a post launch target reselection.
You are going to have quite a lot of work to do to refit Robot Missiles back into the space combat system. You possibly require less in the ground combat system as there is more granularity where Robot options can play into conventional combat.