Pretty sure it has. I've been using the beta 1.6 for a while, and then suddenly SKSE tells me that I'm using a newer version of TES than it supports. Could've sworn I've been playing offline since I updated to the beta.
Might I recommend using http://skyrim.nexusmods.com/mods/12744?
Been using it for the last two patches and it does not let Skyrim update without you giving it permission, even if Steam is online. Works wonderfully!