I find the chronology confusing with respect to the tollhouse and the inn that was set on fire by the goblins and gnolls, to kidnap Ravenheart.
Despite the 1 century devastation, these remained operational. The tollhouse has some diaries of diminishing travel on the road, but that happened much more recently than the Sharran attacks, and the corpse of the master of the tollhouse had been decaying for some time, but certainly much less than a century.
And the inn was still completely operational and intact when the delegation of the Duke arrived there.
So the 1 century of desolation does not quite fit with this.
But it's quite possible that I missed some important info.
So the attack on Moonhaven happened a hundred or so years ago.
Ixal asks above why the village was never resettled. I don't know the answer to that. It's a reasonable question. Maybe the area was overrun with goblins that were never cleared out. Maybe with the fall of the Selune temple, there wasn't much demand for living space thereabouts. But ultimately, it's all guesswork.
Anyway, to address what you're saying, the tollhouse and Waukeen's Rest are modern. They don't have the same history as Moonhaven as they weren't wrapped up in that war/skirmish. The tollhouse just collects tolls from those travelling through the area, and Waukeen's Rest services their needs along the trade route.
However, the trade route is known to be dangerous. That's why traders pay the toll at the tollhouse, specifically because it's the only route that's somewhat protected... or was before it became overrun with gnolls, goblins, and drow.
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Also mentioned by Ixal above, what happened with Khelbun? I don't know the answer to that question either. It's also a reasonable question. Something obviously stopped Khelbun from simply annihilating Ketheric's forces. Perhaps there was some force protecting Ketheric. Maybe Khelbun's hands were tied up in some way. In the letter of surrender, Khelbun does mention that the surrender is being offered to essentially save innocent lives that would otherwise be lost. Or rather, that continuing the conflict would cause more harm than good.
