That is not a measure of how effective they are, but a summary of whether they are filing the necessary disclosure forms and whether their administrative fees are too high or not.

If the EFF lost every single case and donated half their money to their political opponents, then this rating would still be unchanged provided they disclosed everything and didn't take much of a cut for overhead.

AFAIK Charity Navigator takes into account how much money goes to fund raising, management etc, which I would count as efficiency. It's definitely not everything of course.