I agree about the difference. Reading music is only part of music theory, sort of like how learning to read English is only part of English grammar and composition.
For learning to read, the Lil' Rev ukulele method books sort of gently walk you through reading as part of learning how to play the uke in general. If you already have a lot of experience playing the uke, a lot of it might be too basic for you, but still...
For overall theory, including but not limited to reading, check out "Music Theory for Dummies".
JJ