I missed them in my childhood but read them for the first time to my own children. That was a number of years ago and I totally missed the underlying Christian theme. I have a sneaking suspicion that I didn't read all of them before as it's rather hard to miss now.
Well it's interesting because The Last Battle highlights that his reactions to the Islamic people weren't fully like a lot of people. It's also a common criticism to throw up that C.S.Lewis was a 'closed-minded. misogynistic' but as you point out he wrote a lot of feminine strong characters and further he was an atheist who moved into Christianity and therefore I think that highlights a lack of a closed mind if anything.
People like to apply labels to others and then stick them in little boxes whether they belong there or not. For a man of his age, he had IMHO, an enlightened vision of women, and treated his female characters (at least in the Narnia series) as equals to men. I'm sure this alone would have caused controversy.
I have never seen Lewis as closed-minded either. I don't share his views on religion but if reading Lewis has taught me anything, then it is that he was not afraid to challenge his own views at times. To me that surely is not a sign of closed-mindedness.