I find the main disadvantage to disabling the auto-pair quote function is stressing out your syntax highlighting. This is especially obvious if you are editing large files with plenty of text after the cursor. If you type one quote, and it's not auto-paired, there is a noticeable delay while the rest of the document is checked and then highlighted as a string. Once you add the second quote, the rest of the document returns to normal.
With auto-pairing, the two quotes are inserted instantly and the highlighting stays sane. That being said, I've turned off auto-pairing of quotes as well due to conflicts with my muscle-memory