In section 4.3.3 (“Missing and out-of-bounds indices”), the text says:
If the vector being indexed is named, then the names of OOB, missing, or `NULL` components will be `NA`.
But that description applies to single-bracket subsetting (x["…"]), not to double-bracket (x[[…]]). In fact:
> atmc <- c(
+ a = T,
+ b = F,
+ c = T,
+ d = F)
> atmc[["e"]]
Error in atmc[["e"]] : subscript out of bounds
> atmc["e"]
<NA>
NA