So I ask why, to which she replies, "you said you didn't want them in the house."
She may have been advised by an elder or a friend that she needs to abide by your wishes as head-of-household. The brothers also say things like, "We don't want to make anybody mad." Also, WT and Awake! publications are available on cd's now, much easier to store discreetly, if she were so inclined.
In other words, this may simply be a continuation of her 'faith behaviors' and not indicate a change of heart of any kind. I mention this because some of the advice I saw posted, about this being a time to step up efforts to influence, concerned me. That tactic could backfire and force her faith-attitude and behaviors to go 'underground,' creating needless undercurrents of resentment and ramping up a sense of religious persecution on her part.
I would tell her, simply, "I noticed you got rid of the literature in the house. I didn't expect you to toss any of it--though, I appreciate your showing consideration for my feelings." This may be all she needs to hear, to feel like her gestures are positively acknowledged and with no waves of pressure following behind. [She may already be bracing herself for more to come, so she may feel relieved when a simple 'thanks' is all that comes.]
Just my two cents. Good luck with all of this--I know it's not easy.
J-ex-W