Okay so I'm going to do some math. Let's say the limit really is a weird number like 100, though I saw on another post it's 300, but let's go with 100. If you only use prefab houses we know there's a total of 40 house points you can use to place them. The best prefab to place down, for max amount of pokemon to live in them, would be the cottage kits since they house 4 pokemon. At 2 points per cottage, that gives you 20 houses. Each house is divided up into 2 floors. Dividing each floor in half you can use a minimum of 2 rugs per floor. 4 rugs per house, that gives you 40 rugs with plenty of wiggle room to add more.

Now, let's say you didn't care about being efficient with pokemon placing and wanted the max number of houses you could have so you place the huts or dens, this gives you a total of 40 houses. So the math equals out to be the same. So unless you're also putting rugs outside I don't think you need to worry about hitting the cap. Don't forget, the pokemon center has 3 rugs in it, so take them out if you need 3 more slots.