We have be using numbers to "name" our work ever since we could count. If you think about musicians for example, many just numbered their works (Opus No. 106, or Symphony No. 6 etc.). Maybe as a result of that, the aircraft manufacturers followed suit, egged on by the military who used numbers so it wouldn't confuse the officers too much... And it's just carried on ever since then. Numbers are also pretty inoffensive things (mind you, I don't think a BoeBus 69 will ever be built) which is important when you are in an international market. For example, it would a tremendous shame if you spent millions marketing an aircraft only to find its name meant "Nipple" in Russian.