Get in touch with lodilefty here. He may help.
The capital icon can be customized in our recent games, and most likely it should be able to work also in the older games, because the engine is more or less the same...only some special directives are activated or not.
You can make a try for yourself.
Go to GameData/Factions and open the faction file of the nation to edit with a text editor (wordpad)
CapitalSymbol = XXX.png
where XXX.png is the name of your new icon
Run the game and see if it works.