I'm not a hundred percent certain but I think every country is included in FS9, I do know that the North & South pole are inaccessable though.

Most countries are included. Countries like The Vatican and Andora are not on the list because they have no airfields. The North Pole has no airfields either. The South Pole has some airfields which I believe are listed under Antarctica. If you want northern airfields, try searching for ones in the Canadian north (Yukon, North West Territory, Nunavut), Greenland, and Russia.

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Yes.  You can overfly every square inch of the earth with the exception of the extreme north and south latitudes.  "Countries" as such are not "included", in that the international boundries are not shown.  I'm sure Microsoft did this to prevent problems due to disputed boundries (Kashmir and Taiwan being the examples that immediately come to mind).

Actually its a yes with every country that has airports. FS9 also has airports in territories that are not independent nations, like American Samoa or the British Virgin Islands.
The only nations I could find that are not in FS9 and are listed in the World Almanac and Book of Facts for 2004 are three tiny European nations with no Airports: Liechtenstein, Monaco, and San Marino.
Every other nation on Earth is there, plus all of the territorial possessions of the nations like The US, France and the United Kingdom that still have colonies.
The list of nationsl in the Flight Planner is complete.