Annie will be addressed, Libby will not be. Ever, sadly. Libby is the only thing that bugs me to no end about the series (srsly) and the fact that Darlton is done with her -- they say we have enough to connect the dots, wtf? -- makes me nuts. But in a recent podcast, they said they will get to Annie, even if it's not this season... even though this season would have made the most sense for getting an answer.
(incredibly minor SPOILERS ahead; remember, I'm the Spoilerphobe, so for me to be OK with what I'm about to post means it's pretty common knowledge. tag if you think it's necessary)
I love, love, love the podcast. Without outright spoiling anything, Damon and Carlton offer little tidbits on a weekly basis, like answering burning questions -- definitively and humorously -- and letting us know that they WILL indeed get around to most of the stuff we want to know about. When someone writes in and says they want a specific answer, or something/one to be seen again/elaborated upon, 90% of the time, Darlton confirms that their story is not done yet. Again, the only burning question that I wanted answered but they've said they're done with... is Libby. But Annie, the Monster, Jacob, Richard, the Four Toed Statue, Rose and Bernard, the Temple, Christian, and Vincent (and many, many others) will all be seen/addressed again and they will tie them all up as they see fit. They've only got 19 hours left, but I have complete and utter faith in Damon and Carlton. They've never steered me wrong and made me lose faith... except for Libby.