We must bear in mind that any rather small fortified place could be called by the word that the KJV translates “city”: עִיר or ir/ar/ayar, glossed by Strong's as “city, town.” Some readers might not realize that the English word “city” has an older sense meaning any walled or fortified population center, as in “City of London” (the small, old inner London district, now the financial center) and “Île de la Cité” in Paris. This could be true even if, by today’s standards, its population would merit the epithet “village.”
Therefore, it is possible that Hamor ruled a hamlet of fewer than 100 souls, mostly members of the clan and perhaps some slaves—perhaps it was mostly or only “the house of his father” (34:19)—but that the place was fortified. Archaeologists have uncovered fortified places called "cities" which, today, we would describe as little more than forts.
Another consideration makes the mass slaughter by just two men more plausible. While only Simeon and Levi are said to dispatch the hated Hivites, we should not suppose they had no material help from Jacob’s sons and menservants. Indeed, we can assert confidently that the latter did help since we are told so: “The sons of Jacob came upon the slain, and spoiled the city” (Gen 34:27). It is not even inconsistent with the text to say that the other men actually participating in the killing—so long as it was initiated by Simeon and Levi.
We are not told that the two surprised each Hivite individually and dispatched him without a general alarm being raised. In fact, for all we can tell, the Hivite men were rounded up more or less en masse by the Hebrew men, and it fell to Simeon and Levi to act as executioners. We cannot say for sure what precisely happened; that too is consistent with the text.
Then of course we must also bear in mind that, as according to the plan, the Hivites are sore. They also have been recuperating for three days, and are expecting their prince to be able to marry Dinah, suggesting that they would be entirely unsuspecting of a surprise attack.