I haven't even heard of these Beatrice Letters! I'm going to have to track down a copy and read and see if I have a similar conclusion to Karen's.
I never thought of Beatrice being a younger sister. It could be a possibility--although the later books made me think that Lemony Snicket is alive at the same time as the Baudelaires, because all of his sibilings are contemporary (rather than LS researching the Baudelaires long after they are dead, which is what the first books led me to believe). And, if LS is a contemporary of the Baudelaires and a grown man, it would be really weird for him to be in love with their younger sister (younger then Sunny). Not to mention really, really wrong.
But two Beatrice's. That's also an interesting idea. Then one could be the mother, and one could be a sister.
I can't give any more opinion on that until I get ahold of these Beatrice Letters.