Portugal was united with Spain for a considerable period of the game's time span. After that period Portugal was neither a big player in the European political field, nor had it's colony a large influence economically. Calling this empire mighty grossly overstates its importance.
The game merely fields the greatest seafaring powers of the time in a struggle for the New World. Sure, The Netherlands claim on present colonies is small compared Portugal's claim, Brazil. The fact is, however, that Portugal was never in any large conflict with one of the other European powers at the time. It is likely that if the Netherlands hadn't played such a major role in the political conflicts of the time, Brazil probably wouldn't even speak portuguese nowadays, as the French and English attempts at colonizing Barzil would have been far more successful.
Furthermore I doubt leaving out the concept of slavery was the reason for leaving out Portugal, Everyone, including The Netherlands, dabbled in slave trading at the time. I also doubt the ancestry of the would-be buyers of the game played any role in including the Netherlands and not Portugal. If they wanted to sell the game it would have made more sense to include Germany or Italy, a lot more people of that Ancestry in the Americas then those of Dutch ancestry.
I, in conclusion, maintain that the four powers included in the game simply represent the most powerful seafaring nations, although in present times the cultural impact on the Americas of some of these nations may seem less than that of Portugal.