Snippet from http://www.skygod.com/asstd/abc.html:

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Some special interest groups successfully lobbied the government to obtain their own special letters. The Navy saved all the new ‘N’ codes. Naval aviators learn to fly at NPA in Pensacola, Florida and then dream of going to “Top Gun” in Miramar, California (NKX). The Federal Communications Committee set aside the ‘W’ and ‘K’ codes for radio stations east and west of the Mississippi respectively. ‘Q’ was designated for international telecommunications. ‘Z’ was reserved for special uses. The Canadians made off with all the remaining ‘Y codes which helps explain YUL for Montreal, YYC for Calgary, etc. One of the special uses for ‘Z’ is identifying locations in cyberspace. What am I talking about? Well, an example is ZCX the computer address of the FAA’s air traffic control headquarters central flow control facility. ZCX is not an airport but a command center just outside Washington D.C., that controls the airline traffic into major terminals.

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I remember an even better explanation in an old issue of Airliners Magazine but I can’t find it right now. Anyhow the Y series is a very old designator and it is also used in the ICAO four-letter codes, with e g Montreal-Mirabel being CYMX but YMX in IATA language.