A friend of mine found an 1482 English coin in a playground in Hayward, California in 1980`s with his metal detector.. This had been part of San Leandro Bay before it was drained and used for houses etc in 1800`s. The playground would have been the bottom of the bay then coz it was shallow enough for a vessel to enter- My hunch is that Drake used San Leandro Bay to repair his ship coz it is very quiet there and the waters are still enough for such work and the Ohlone Indians were there...
It could be, as Drake’s logs were kept by the Crown upon his return, and lost in the 1666 Great Fire (apparently; lots of stuff apparently was). Various summaries of his voyage have survived, but they lack both exactness and the kind of persistence that would have come from repeat voyages.
Of course, coins tended to stay in circulation for a very long time, so it may have been lost long after, as well. Might be worth another look, for artifacts.
http://www.google.com/search?q=francis+drake+landfalls+site%3Afreerepublic.com