Yes, it will carry over fine. The URL is generated on the fly. You'd probably need to do an htaccess rewrite rule however for anyone that actually links direcly to the pictures, so it goes to the new location.
The main reason right now it's a set directory structure is to accomodate safe_mode, since it's not just a matter of creating a single directory as it is with the avatars and file uploads, it needs the directory structure that I mentioned earlier.
