Rob might come along with more detail, but it's to do with the silver being used in the coins. I think the VIGO silver was captured by Admiral Rooke from the Spanish or French (accounts differ) in Vigo Bay, and the LIMA silver was captured from the Spanish by Admiral Anson.
Also, I think it's correct that VIGO was the first time that a word was used on a coin to denote the origin of its silver, as opposed to Roses, Plumes etc.
I wanted one of each, because of the historical interest. I have a 1723 SSC (South Sea Company silver) shilling and a 1739 Roses (West Country mines silver) shilling, both of which are pretty common. I would like a Plumes (Welsh mines) shilling as well, ideally a Queen Anne one of 1707 or 1708. One day!