In order for scouts to increase knowledge in a country they need to be able to attend matches. As Nigeria and Ivory Coast don't have active leagues in the game, the only matches the scouts can go to is the national teams and perhaps if a team is in a continental competition. Your scouts are basically attending an international game once a month which is why it only reaches 3%.
TBH it's not worth scouting these countries individually currently in the game, it's better to find staff of that nationality and hire them then use player search to find youngsters, or scout the African cup of nations etc.
This is a bugbear of mine as the game doesn't tell you this anywhere.