Indeed. Moreover, aside from the performance and security, there's another important factor to take into account. And that is the fact that IDs can contain characters that have special meaning in CSS selectors (such as dots).
We've seen this in before when dealing with a MediaWiki heading (where the ID-version of the heading can (or could) contain dots). So whenever you have what is supposed to be an element ID in a variable, use document.getElementById (even if you don't care about performance or security).
Modern browsers like Chrome / IE9 are really fast, jQuery isn't just about performance but also about shorter code. Why don't have something like $.id(myId), as a "shortcut" to document.getElementById(). Also perhaps another .get* methods (there were bunch of them). As you are one of jQuery code maintainers, such feature can be easily implemented. Dmitriy