Well, this peculiar acronym expression stands for "Ok" or "message acknowledged". It is the same as nodding in person or saying "gotcha".
The other bit of history behind "kk" is the 1990's expressions "k, kewl". Translated, this expression meant "ok, cool", but was stylistically spelled otherwise. "k, kewl" undoubtedly also influenced the use of kk in today's online chatting.
The kk expression, like many other Internet expressions, is part of online conversation culture.