Deep meson sites are easily "built"... Pick a spherical hull. Install a spinal mount meson, PP, bridge, computer, and quarters, and a bit of on-board fuel. It is axiomatically Agility 0. Keep in mind it can only be targeted with meson weapons. ...
If I recall, in canon the deep meson site could only be taken out by taking out the sensor sites feeding it targeting information. By MegaTraveller rules, Zhodani densitometers could only penetrate about 250 meters, Imperial densitometers up to a kilometer. If you could get below that, the unit could not be found.
Except ...
The meson site requires power, a lot of it. Fusion power plants put out neutrinos, which under MegaTraveller could be picked up by neutrino sensors. Assuming the power plant is similarly hidden and effort made to discharge heat well away from the reactor itself, a TL 14 10 KW neutrino sensor acting alone to locate the plant is a
difficult task, base roll 11 plus computer rating, minus range in 25 thousand kilometer increments, so basically pretty easy from orbit given an adequate computer. Gaining a lock is basically the same but a
confrontation, which rule I find more than a little confusing in this context because the DMS listed are for
offensive computer and range ...
Difficulty, Off = computer model number; Def = range (confrontation, uncertain).
... which I think means the attacker rolls with a bonus for his computer, while the defender rolls with a bonus for range, with the high roll taking the prize, though the attacker can get a little info out of it if he rolls close. In this context, assuming a ship with a good computer in orbit within 25 thousand klicks of the planet, lock is almost certain. Ergo, taking out the power plant feeding the deep meson site is not particularly hard if you're willing to expose your ship to return fire and have mesons of your own to apply to the task.
The power grid may be decentralized, with several plants feeding that and other weapon sites, maybe even city power available as backup, but it's only a matter of time before you knock out enough power to take the thing offline. There may be non-nuclear sources, but finding something non-nuclear that puts out power in the 1 to 3 hundred thousand megawatt range while remaining inconspicuous from orbit is rather challenging.
But there aren't any defined rules for detecting deep meson sites, nor has there been much discussion about how to detect space ships from the ground, how the planet and it atmosphere etc. may affect detection range and/or sensitivity for the various sensor types.
I don't know of any rules addressing atmospheric impact on EM sensors. Seems to me that'd be a problem, not insurmountable, but ground-based passive sensors might not have the range that space-based ones would. However, neutrino sensors won't be affected by that. Under MegaTraveller, neutrino sensors are best in conjunction with EM sensors, but they can be made to work alone at higher techs - just with some loss in range. At TL 14-15, it's a base 11 on 2d6 with bonus for computer rating and penalty for range in 25,000 km intervals (so 3+ for someone in orbit at TL 14, 2+ at TL 15). As for weapon lock, it's as easy for a ground-based neutrino sensor to pick up a ship's power plant as for the ship to pick up ground-based power plants.
If we assume passive EM is degraded by atmosphere, this creates a situation where ground-based batteries don't have as much range as space-based weapons - but space-based attackers are going to have the same problem picking out ground-based targets, perhaps moreso since they're having to do so against the backdrop of a planet while the ground-based defender's trying to identify something floating alone in vacuum. This leads us into the canon situation where attacking spacecraft are having to get in reasonably close to the world to attack targets on the surface - and thereby coming within range of ground-based fire - while defending ships far enough out in far orbit may be outside the protective umbrella of shore batteries.
There's the suggestion of use of densitometers to hunt for sites, but I fear they could be easily spoofed (build empty holes in the ground with empty tubes).
There's also doesn't seem to be a reasonable counter to a DMS if the attacker does not have meson weapons.
Other than locating the power plants and sending down troops to destroy them.