Question:
Are major city hexes considered non-clear terrain?

Answer:
No, major cities do not contain clear terrain.  They are a terrain type, not a feature.  Features exist within the other terrain of the hex and do not change the basic terrain type.  For example, you cannot have a “dot city hex”; you simply have a dot city existing in a hex of whatever terrain type it is.

Source:
[Rules Court, TEM 62]