You post guards at the edges of your base, not in the middle of the living areas. And even if the Uchiha had posted a guard force of its own (which is understandable considering they planned a coup) it would have probably been 1-2 person teams scattered around, easy pickings for Itachi to take out one at a time.

As to the numbers I wouldn't put them above a few hundred, does anyone have an extended family of 1000 people? A few hundred is still a lot of people to kill in one night but two people killing a few hundred surprised and off guard people in their sleep seems within the realm of shounen manga feasibility.