My wife and i have been atheist for many years now.... we never told our kids, but we always encouraged their questions to get them to think for themselves. Our two eldest kids have (in their own time) voiced their doubts about faith (we were all originally Roman Catholic). When they came to their individual atheist conclusions, we came out and told them that we too were atheist.
Our youngest, however (she's 13), seems to be clinging on to faith. she asks us to pray with her... and I feel sorry for her, because we don't attend mass anymore (for years now). I think she suspects, but she hasn't asked us about it. I think she has her doubts, she mentioned that her best friend thought that there might not really be a god, but she didn't ask us what we thought. I think she's fishing. But I don't want to open the subject. with the other two kids, we waited for them to ask the right questions. Our youngest isn't doing that... at least not yet.
Well you can continue to go with your gut. Personally, my 13 year old would get the truth but that's our family. I just wouldn't hide how I felt about religion from my kids. What I did do a lot when they asked questions was ask them what they thought and why. Then tell them what various groups of people think and finally, what I think and why.
The best thing I can say about it is if your daughter is commenting on what her friend is thinking, it may be good to respond with a question, like "What do YOU think?" My husband and I use this as a teaching tool for our daughter in many aspects of her development, not just theism/atheism. It helps bring up the thoughts to the table. She may just be nervous to ask you outright and is looking for a way into the conversation. Stay neutral if you can, and help her through it.