I don't think this question is unsalvageable (and indeed, has received a phenomenal answer despite that), but the underlying premise of the question as it currently stands is a poor one.
Is there an in-universe explanation why nuclear bombs are so weak in StarCraft? With the scale of the explosion, and the damage done, in does not seem bigger than an average mortar shell in real life.
Should I understand the in-game buildings as vast cities, and the in-game units as large armies, or are nukes really that small?
The first problem this question has is an issue of relativity. The contention: "Starcraft 2's Nukes are small" is an assumption. How many "in-universe" people does 1 marine equal? Is it one-to-one? Does each marine represent a squad of 20? How many miles are represented by an in-game unit of distance?
Such relative comparisons are unknown, and unknowable. There is no way to compare a game-mechanic (i.e., the size of the nuclear missle radius in distance units) to a real-world phenomenon (i.e., the size of a nuclear missle radius in kilometers).
By in-universe explanation I mean something different than "it would imbalance the game if one bomb could destroy everything on half the map."
The question also makes the assumption that the game was balanced around the size of the nuclear missile, instead of the reverse. But worse than that, it expressly forbids the only "real" answer available - that the size was mandated by game balance.
The bottom line is that this question isn't really asking about starcraft 2's lore at all. It's much more a question of, "This videogame doesn't match my view on reality. Why?" I'm not worried about this individual question so much as I'm worried about the precedent of allowing questions like this in the first place.
In short, I see this question as more of a rant about inconsistent storytelling than anything else:
The answer leaves 2 open questions: 1: what about the rogue factions, are they bounded by that law too? 2: This law was made before the big Zerg wars (maybe even before mankind's first encounter with the Zerg), so won't these new circumstances allow for, let's say, destroy all life on a planet if it's completely taken over by the Zerg (and no other life firms remain)?
Both of these "open questions" are purely speculative.
This question has very little to do with Starcraft, and much more to do with how something in Starcraft isn't what the Asker expected it to be.