The reasons for using them are many, and some has been mentioned by others.
Another one that mole125 more or less says is that you may have picked caches from different searches at Project-GC, and want to know why you added that specific geocache. So that you in the field can chose which ones to skip if you don't have time.
For example "rare date", "favorite", "X needs the DT" and so on.
And no, they are not included in the GPX and will not end up in the GPS. To be honest, if we would add all the things into the "fake log" for the GPS unit that has been reqeusted, it would be a very long log by now. In this case I would suggest bring a paper with the list as a complement. This wlil probably give a much better overview than looking through 50 caches in the GPS unit anyway.
We are of course always looking for and listening to feedback. This has been designed after how I geocache myself, and from the feedback we have had. When I visit a new area, I usually handpick geocaches with VGPS, and I usually do have some form of paper or digital document (google docs) that lists the geocaches I want to log.