Pretty much for the same reason that you rarely see truly global chat channels in these games, and why the Trading Post will only show you 10 items at a time. The computational complexity of scaling player services is exponential, so with larger numbers, it becomes quite easy to exceed the capacity of your servers. If you think about it, the servers that handle things like guild chat are under a never ending DDoS attack.
As an example, look at something simple like hitting the 'G' key to bring up the guild panel, which shows you the current online and representing status for every member in the guild. Today, when you hit 'G', the server has to parse the list of all 499 guild members (minus you) to check that status and send it to you.
499 record lookups is nothing for modern hardware, but what happens at scale? Let's say there's a huge event going on, and everyone in the guild is online. Someone says in guild chat "lol Fog rolled a thief", and 499 people (minus Fog, who knows darn well that he rolled a Thief) hit 'G' to check it out. The server now has to do 499 record lookups 499 times - that's 249,001 lookups, just shy of a quarter million, and send out 499 client updates. My computer takes 1.07 seconds just to read 250,000 bytes from a file, without actually looking anything up or doing anything with that data.
Now imagine that Anet increased the size of a guild to 2000 members, enough to house all current GW2 Gaiscioch, with room for reasonable growth. If Fog then rolls an Engineer, the server has to do 1999 lookups 1999 times - just short of 4 million lookups. My computer takes 7.51 seconds to read that many bytes, and do nothing with them. So, by increasing the guild size by 4 times, they've decreased the performance of one player service by over 7 times. The numbers only get worse the more players you add - it's over 3 minutes with 10,000 members, hooray for exponential growth!
That's one guild locking up one player service for several seconds. Compound this over all the other guild-related player services for all the other guilds on the server, and the game could become unplayable.
Obviously, this is cocktail napkin engineering, but the principle is sound, and hopefully it sheds some light on the performance aspect of the guild limits.