To me it sounds as if an outside pouch is a much better idea as your daughter will have easy and immediate access to it at all times. I do not think that she has to be the least bit concerned that her Siddur may come into contact with other bits of luggage as it will be in the pouch and out of the way. However, I think that it would be a good idea to put the Siddur in another bag before it goes in the pouch that way there is a little extra protection and the bag will serve as a second covering so that it can be taken into the bathroom as well if needs be.
I hope that your daughter has a memorable and inspiring trip!