The Intertubes ate my post!
There has been commerce between Spain and Italy since before the Romans conquered the next tribe over; this sounds like an exaggeration until you realize there were Greek colonies in both places, and before that the Phoenicians and before that the people of Crete…
Different monarchs of Spain held posessions in Italy (both North and South, although the longest hold was in the South) through the late Middle Ages and the Renaissance - this combined with the commerce and with the two large pilgrimage routes (to Rome and to Compostela) to make it not-totally-unusual for people to migrate from a country to the other even during those times of bad roads and worse sailing; the Borgias were Borjas both before and after they had some of the most famous and horrible Popes, just to name a famous case of migration between the two countries.
As for Núñez de Balboa’s name, it seems a curious case. My first instinct when I see that structure is to assume that “Núñez de Balboa” is what we call an “apellido compuesto”, with a structure commonly found in central-northern Spain: “commonlastname from place”. It seems to fit. But I can’t find a place called Balboa, and some internet-based research (so not necessarily trustworthy) says that it’s actually a much-older structure and not a family name: “sonoffather’sfirstname from place” (Vasco’s father was called Nuño Arias de Balboa - the Arias is not a patronymic) and that the place in question happens to be a castle near the town of León, in Spain and close to the NE corner of Portugal.
It appears that anybody, Italian, Spanish or what have you, who has the toponymic Balboa as a lastname would be descended from people born in a castle near León.
Out of curiosity, I checked the Spanish White Pages: quite a few entries for Balboa just in Madrid (curiously enough, INE, which would in this case be the equivalent of the US Census, says there isn’t any province with more than 20 Balboas known to live there). Italian White Pages: three people, two businesses. Portugal: nothing.