It's relevant to maintenance and repair of ships. It is largely irrelevant to the defense of the planet. ...
Agreed, but the question I put forth was: how do you keep the naval base from being destroyed? The fate of the naval base is presumably irrelevant to the folk on the planet, who would just like the enemy warships in their orbit to go home and not bomb them, but it's the issue I'm focused on.
What I have so far is: land them or put them out where they can jump away. Base elements located, say, a half day's flight from the mainworld, equipped with 1G maneuver drives to keep moving about so their position can't be predicted and a fleet jumped in on top of them, equipped with Jump-1 drives and adequate fighters or escorts to watch for inbound attackers so the element can jump if someone tries to get at them through normal space, they'd be pretty hard to destroy, and they'd remain functional even if the mainworld was besieged. Probably also a good idea to have dispersed and redundant assets, back-up elements in deep space just in case one of the elements is destroyed.
Might also be useful to give them a few monitors under their own command to keep the occasional raider at bay, if the base is at one of those worlds that don't have enough strength to do that job but, if they're sufficiently hard for the enemy to catch, that's not needed.
...Destroying the naval base simply means the ships have to go elsewhere for maintenance and repair. ...
That can be a significant strategic achievement. Making a fleet take two or three jumps to get back to a repair center would seriously handicap that fleet's offensive operations.
...So, the defenses of that subsector would be concentrated in the important systems while the second tier ones would get some defenses and the rest are left to their own devices. ...
That sort of defense strategy leaves a salient like Jewell vulnerable to being pinched off. Take Nakege, Lysen, and Mongo, and Jewell is cut off. Certainly Jewell could stand on its own with enough defensive forces, but the locals might wonder why they're bothering to stay in the Imperium after a couple of decades of having no contact with them. The fortress system's a good starting point, but you still need a powerful force to re-open the routes to them, and that force is going to need bases close enough to the front lines to serve their needs.
Well this always begs the question whether fixed defenses are viable for planet defense anyway, vs active ships in space...
I'd vote for yes. Fixed defenses are cheaper, for one thing, so more bang for the buck. That can mean a lot in the opening round of a fight. A second issue is, as you pointed out, "Laser, Energy, and PA weapons are all compromised by atmosphere." Ground-based defenses don't have to worry about being degraded by attacks from those weapons. Third - if you accept canon descriptions of deep meson batteries - those batteries are out of reach of opposing weapons. Likely the associated computers are as well, buried with the weapons. Most of the electromagnetic-frequency sensors can be targeted if spotted but, if they have neutrino detectors as described in MegaTraveller, those sensors are buried with the gun and out of reach as well. Mass detectors are vulnerable but may be impossible to find; there's no reason to believe they'd need something like dishes that could be visible from orbit to do their jobs. (You could come up with some rationalization for requiring mass detectors to have exposed elements if you felt the deep meson was too deadly otherwise.)
Power can be located and targeted, but they can be buried beneath the reach of weapons besides meson batteries, and if you disperse the power plants - imagine a 1200 EP power plant as 1200 1-EP power plants scattered over a wide area so that only one can be killed at a time, and a couple hundred extra plants to keep the weapon operational while the first few plants are being destroyed. That's something a ship can't do because everything has to be inside the hull. It's much easier to silence a gun in orbit than to silence one buried beneath your reach and powered by a well-dispersed network of power plants. Frankly, I can't see how you'd win such a battle except by landing troops in numbers sufficient to overwhelm the local army and then using your troops to dig out and kill the power plants and such. Stuff in orbit is just so many clay pigeons.
Missiles aren't as useful once dampers show up, but you're right - the image of a thousand batteries opening up from sites scattered all over the planet's
surface would certainly be daunting, especially to the troops being landed in boats and APCs.