Diplomatic isolation, not geographic isolation. Africa's pretty much in the middle of the world- geographically, it's probably the least isolated continent on earth. And as for the second question- there were plenty of significant African ports in the Atlantic. Most of these were superseded by the trade ports which were established by the Europeans, such as Lagos, Bissau, Luanda, Conakry and Cape Verde, but most of the other port cities in the area, such as Accra, Abidjan, Banjul, Ouidah and many more, were established by the Africans, not the Europeans. And there were a few special cases like the
Bidyogo, in present-day Guinea-Bissau, where the local Africans did have pretty powerful navies, navies which were capable of routing and repulsing repeated invasion attempts by the Europeans until well into the 20th century.