Email via BIS does not sync, which is what you are asking about. RIM has agreements in place with some providers, i.e. Yahoo and gmail, that will allow it to happen. They might have had such an agreement with Microsoft for hotmail. There have been a considerable amount of problems with hotmail and the BB and I tend to think it is an issue they must resolve themselves before hotmail users will see anything different.
I do not know of a fix. You can always hit the SEARCH button above or use Google to see if there is anything that can fix it. Start here: Hotmail Sync & Sent Items etc... - BlackBerry Support Community Forums