I think there is no signifcant problem as long as you keep your wits about yourself. Anchoring in an isolated lagoon in one of the dangerous spots is not a good idea maybe - but it is hard to find those isolated spots anywhere. I don't follow the US travel advisories but check the Canadian ones and I have found that they are very conservative in their recommendations - as they should be. I remember their recommendations for Ecuador were concerning before we went there and I have rarely felt safer anywhere than I did there. People were incrediblely friendly and helpful and went out of their may to make sure you knew where you were going. I suspect Mexico might be similar.
Finished the circumnavigation in early February in Grenada. Have to work on a book project for the next several months so the boat will be waiting for next year.