You're right, Haruka, you could say 'every' here. Grammatically it would be correct, but the focus would be slightly different.
If you said 'every one' you would be talking about the building as a whole and the total number of apartments, and the fact that 100% of the apartments have balconies.
If you say 'each one' you are considering the apartments individually.
Don't worry too much about the difference, though, as it is very subtle. And no, it doesn't matter whether there are six or sixty apartments.