To reply to your first question, don't take anything in the game to be historical... The mission, for example, is given to you simply because it makes "in-game"... Venice at the period was a greater power than Portugal and its merchants were more far-reaching than Portugal could ever hope to be...

To answer your second question, the key to successful merchant buy-offs is training...

You'll have to train your merchants to a level of 5 finance at least to be able to acquire lower skilled merchant (that is level 0 to 2)...

One of the quickest way to train those merchant is having a merchant guild and obtaining a monopoly on a resource or sending them traveling far away to get good traits... Once they have reached a high enough level, taking out enemy merchants will rise their level higher still... and so on so forth...