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.
True, but some non-nuclear sources (as geotermical ones) may be used to recharge batteries and allow for some sporadic fire (maybe fro 2 shoots a day to 1 shoot every 2 days).
It seems not much, but planetary invasion may take a long time, and this could be eroding the invader fleet on the long term.
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.
The sensors use in atmosphere (and gravity well, for densiometers)was highly discussed in this thread.
Other than locating the power plants and sending down troops to destroy them.
Or to destroy the sensors.
I also believe that there are some war regulations in the way to your don't use your deep meson sites as a guerrilla and I won't need to leave all your civilian population without power to silence them or something similar.
We tend to forget about the civilian population a planet has (and that is usualy what makes the planet valuable), and that can be used as a bait (if you force us to make a costly assault the civilians in the zone will suffer the most).
Of course, political reasons of fanactism may overrule those conventions (as in IE or in the Rebelion at large, mostly while the Black War), and results use to be catastrophic (mostly for the civilians caugth in the middle).