...for a world, one answer seems obvious to me: kill everyone. I'd say that, at that point, you've conquered it.
But killing the defenders is the very thing the defenses prevent you from doing.
Say, you manage to slip a Genesis device through those defenses and kill all twelve billion people down on the planet, while mutating said planet to one ideal for your species and its needs. You still haven't defeated those well-shielded defenses in orbit, and you still don't have access to the planet. A conquest has not taken place until you remove the defenders. And the defenders by definition aren't a soft target, even if a planet may be.
One way to get around the defenses would be to blackmail the population. But while a single starship in orbit can do that in fantastically many ways, the life expectancy of single starships in defended orbit is apparently counted in milliseconds.
Perhaps the invader could slip in a biochemical poison of some sort with a saturation missile attack, then withhold the antidote until the defenders capitulate? The thing is, we haven't seen saturation missile attacks in action, so we don't know exactly how defenses would cope with those - or even whether the defenses happen to be so good at dealing with those that our failure to see any such attacks simply directly follows from the fact that they can't be done.
We've seen a single vessel poison the atmosphere of a while world rendering it uninhabitable for a particular species, so that's one approach.
But that's against planets that are undefended. Since every invasion worth the name involves hundreds of starships, and a force of two dozen is explicitly declared too small to be for invasion in "Redemption", it sounds safe to assume that invasions in general face defended planets and cannot be conducted by single ships per planet.
Were there proper and apparently common defenses in place, you'd probably have to fire a million projectiles at the world to get one poison canister down there, even if the one did suffice. This may be one reason why genocidal weapons don't enjoy particular popularity in Trek: you can only afford so many silver bullets, and you really need to fire those from a Minigun. The other reason may be that "slip-through" weapons that do noticeable destruction don't help with getting hold of a planet's resources, as they cannot be used with any sort of precision.
Just what the hell is the Mars Defense Perimeter anyway? Is it seriously just three pods that attempt to intercept an intruder? And what happens if the attacking ship approaches on a vector that doesn't go anywhere near Mars?
The name itself sounds descriptive enough. It defends Mars; and if the attacking ships are vectored elsewhere, then it is doing its job admirably!
No doubt it features a broad range of armaments, with a little something for every invader. It just happens that gigantic indestructible cubes full of cyborgs won't mind most of those defenses, being something of an outlier as threats go. (I gather those missiles would have been excellent weapons against Space Amoebae!)
The bottom line in general seems to be that defenses trump invasions by a massive margin. Else there would be far more invasions, conducted with far fewer resources. Not to mention a lot more "sub-invasion" attacks, such as terror bombings, which never seem to happen in Trek wars (only in domestic quarrels like the Maquis hunt).
Timo Saloniemi