Yes, there are atheists in fox holes. I served four years with Amphibious Squadron 6 out of Norfolk and Little Creek Virginia. I was forced when I joined to choose a religious denomination. I told them I didn't want one, but they told me I had better or else, so I chose Presbyterian, and now it's imprinted on my dog tags.
Here's a nice article from the Stars and Stripes titled "Military atheists want new rules on prayer"
It's a long time coming.