I have INCREASED the costs of some select units in the late game (iExtraCost in Civ4UnitInfo.xml is extra gold cost per turn).
Gunship, Carrier, Missile Cruiser, TacNuc: 1 gold
Stealth Bomber, Battleship, ICBM: 2 gold
With guided missiles adding to your unit count, I think it's quite appropriate for the extra expense they incur.
Before BtS I had doubled the cost of units (iUnitCostPercent in Civ4HandicapInfo.xml 100 instead of normal 50). Have left it at 50 for BtS.