Kinda unofficially deprecated. Sortof.
Reason being that with XHTML and XML, you have the XML declaration at the top, delimited by <? ?>. When short_tags is turned on, PHP chokes on this line and you have to kludge some sort of workaround if you want to embed PHP in XML pages.
But that's pretty much the only reason short_tags is turned off by default. It's the only reason I don't use it.