I asked an online children's literature list that i am a part of the question of the missing 'Queen' and whether it existed before. One guy wrote back saying that his edition, a 1956 thrid printing by Geoffrey Bles, the original publisher (later bought out by Harper), does not have the 'Queen' in it.
This means more than likely that Lewis just wrote "Susan the Gentle".
The reason, as has been mentioned in this thread, was probably just because he didn't feel like putting Queen in front of her name. I doubt there was any hidden reasons for his decision as he was just writing this book with no plans for any future Narnian Chronicles.
MrBob