It's my understanding (yet I'm not expert by any stretch) is that software like Adobe Camera Raw effectively maps out or masks hot pixels automatically as it reads a RAW file. Earlier versions of Aperture did not include this feature. I know iPhoto currently does and Aperture 3 appears to as well. In iPhoto, when you first load a RAW photo, you can see the hot pixel, then it just goes away in a few seconds. Its always there when u re-open the file for a moment, so the RAW files is not being modified. iPhoto is just re-applying the mask or whatever you want to call it - and a jpg created from the RAW file will automatically be fixed as well.
If you view a RAW photo that has not been processed to remove a hot pixel, then it will probably look worse than it's JPG counterpart since jpg compression will probably make it stand out less.