What is the first metaphorical use of “alphabet soup” to refer collectively to some kind of diversity? Does it date any earlier than the film “North by Northwest”, in which the expression is used by the Professor to refer collectively to the highest-level intelligence services of the country?
My guess is that it comes from the soup with alphabet-shaped pasta in it, Alphabet Soup. As Wikipedia says:
Alphabet pasta, also referred to as Alfabeto, Alphaghetti or Alphabetti Spaghetti, is pasta that has been mechanically cut or pressed into the letters of an alphabet. It is often served in an alphabet soup, sold in a can of condensed broth. Another variation, Alphaghetti, consists of letter-shaped pasta in a marinara or spaghetti sauce.
A similar product, Alphabetti Spaghetti, was sold by the H. J. Heinz Company for 60 years before being discontinued in 1990.
Now, any group of agencies that identify themselves with their acronyms tends to appear to people as simply "a whole bunch of letters". So referring to the security agencies (NSA, CIA, FBI, and what have you) as an alphabet soup simply invokes the image of a whole bunch of letters on your plate.
Wikipedia calls it a metaphor:
Alphabet soup is a metaphor for an abundance of abbreviations or acronyms, named for a common dish made from alphabet pasta.
Similar expressions that indicate the tendency to overuse acronyms are YABA (Yet Another Bloody Acronym) and TLA (Three Letter Acronym, used to generically denote any such organisation or agency).