It's harder to hide the guns on a lower pop world. Not the guns themselves, but their support infrastructure - the basing for their crews, for the techs, and those that support them, the transport facilities and buildings that support them, and so on. It's also harder to hide the networking, the sensors, and the command systems that let them 'see out', and it's harder to hide the power supplies and their waste heat. Likewise, it's harder to hide the firing signature of the gun. The smaller the population, and the less industry, the harder it is to hide the guns and their infrastructure and support.
And yes, they won't be the only means of defence of any world serious about defending itself. Missiles and beam weapons will be there too, and at high TLs vehicle mounted meson gun artillery could be linked into the defence net and used against ships and landers at shorter ranges.
Where did you draw this information? It doesn't sound like anything I've encountered in canon. Speculating? Or maybe a version I don't have?
Crews and techs can be dug in deep with the weapon. If you can dig in the weapon, you can dig in the crew and such. If you can't reach the weapon, you can't reach them. We did that now with our Cheyenne Mountain complex and with the crew bunkers manning our land-based missile silos; probably not as effectively as some higher tech military could do it, but the concept is clear. You could starve the meson crews out - eventually, maybe, depending on what we're saying about artificial food production from waste, and I don't know what Traveller says on that subject - but civilizations that can build spaceships and fusion plants aren't going to have trouble building self-sufficient deep underground habitats, even if it means stocking them with a year's supply of MREs. Their only real problem is fuel, assuming you find a way to isolate it from underground water sources. CT is quite clear that deep mesons can't be targeted, so there's no "the smaller the population ... the harder it is to hide the guns ..."
I'll toss you a bone here: MegaTraveller and Classic Traveller handle it differently. Classic Traveller is clear that you silence them by finding and destroying their sensors, and there's nothing I've encountered in CT that says it's harder to find those sensors on high tech worlds rather than mid tech worlds. It's easier to silence guns if there are fewer of them, ergo fewer sensors, so population is really the main consideration: how many guns can they support? There's also nothing that says you can silence mesons by destroying their power sources; power sources can be dug in deep with the meson batteries. You destroy the sensors, and you either do that from orbit while he's shooting back, or you get troops to ground and have them do it, and it's a lot easier to get troops to ground if you can first send in special forces in tiny stealthed capsules that can get them through planetary sensors so they can land and do their job of silencing enemy missile launchers that could target landing boats and grav vehicles while they're still in space making their way to the planet. As for the military's shorter range weapons, well, your military has those too; that's why it's called a battle.
MegaTraveller though - MegaTraveller has neutrino sensors. This radically changes the landscape. Neutrino sensors are passive, and they don't care how deep underground they are, so they can be buried with the gun. On the one hand, it means there's a sensor you can't detect, so it can't be silenced and the gun can't be stopped by killing sensors. On the other hand, it means you can use that same type of sensor yourself to detect and lock onto his power sources. Oddly enough, MegaTraveller's process for battling deep meson batteries does not take that into consideration: it still says you have to kill the sensors, and it makes no allowances for killing power or for sensors you can't find. That probably deserves errata, but that game really isn't being supported much anymore; everyone's moved on to the other stuff56w3]'e. But, yes, in an MT setting, you can hypothetically silence a meson PD gun by killing its power - it's just they're likely to spread that power around by making many small plants, so you're picking off power plants while he's picking off your ships. They're also likely to dig them in deep so you can't kill them easily with weapons other than mesons. Troops are no help against meson PD in an MT setting - which I think is a problem they didn't anticipate, but MT had a lot of problems.
Alternately, we can forget canon and make up our own rules. I know of no "firing signature" for a meson weapon unless we speculate that there'll be a line of decayed mesons along its path of fire that can be used to trace it back to its source, and then we're saying we can in fact detect the deep meson battery and shoot it with it own mesons, once it's fired a couple or three times so we can triangulate. That might be more helpful than trying to take out many small power plants, but it would take a house rule kind of thing.