I have encountered the ATOM
type in the Win32api and also in the Acrobat API there is ASAtom.
As far as I can tell, atoms are keys for a hash table usually
The earliest thing I can find about the term "atom" is from the Lisp programming language (source). However, it probably originally came from mathematical logic. In programming they are also called Symbols and at its simplest form are name integers (an enumerated type in C would be an example). However, they are widely used in many programming languages and in the Win32 API and Acrobat API they are identifiers for strings in a table.
Also, as Mehrdad points out, the original meaning in Greek is "indivisible", so they imply a primitive data type which cannot be broken down any further.