It is all down to the the early days of the telegraph where messages were paid by the letter. To avoid unnecessary costs words were often abbreviated, X was chosen to end the abbreviation as it was an uncommon letter in normal use. This probably started informally amongst the telegraph operators who were incentivised as they were paid per message sent. It was eventually officially adopted by the telegraph companies and subsequently by radio telegraph operators. Radio and telegraph operations were then coordinated wordwide by the the formation of the International Telecommunications Union (ITU) who still regulate radio operations today.
One of the main things they coordinated in the early days of radio was the use of radio on international transportation introducing amongst other things a system of callsigns for radio stations. Each country who was a member of the ITU was allocated a call sign prefix, either a single letter, two letters or a letter and a number. Eventually these callsign prefixes also were used as the initial letters for civil aircraft registrations.