The Map of Sparta according to me grows to a square(though is rectangle most times). The 4 sides of this square keep on filling on an algorithm. A new city will always form on a side either at the horizontal or vertical edge.
The theory with bot cities was that those cities were formed in succession through repeated mouse clicks(hacker stuff here). This caused creation of large number of cities through in quick succession. Thus forming a line of cities. You can see in the map that how those bot cities are in the form of a square. Some bots must be created earlier and others later thus forming different squares.
And this map does not include all the bot cities in sparta, not the line i use.
Well, the illicit use seems to have created a bonus for other players, bots are known to plarium from a long time, they must have for example, banned those accounts from the hacker owners or have taken any precautionary measure. So, no illicit advantage must have been taken of.
Checking Hermes and Towers down is only 1 factor in deciding whether the city is inactive. Dangerous players have their Hermes and towers down.