In my opinion, they don't. If you use an IDE like Eclipse where deprecated methods are clearly marked by a strikethrough and marked with a compiler warning, I don't see the big deal. And the bonus is that old code still compiles with new versions (and there is something to be said for backwards compatibility, a la "This presentation is not compatible with Keynote" discussion from a few days ago)
I don't believe they have ever removed a Class or method from the JDK... Thread still has all of those super-unsafe or non-implemented methods in it (see: stop(), destroy() etc.)
I think part of the reason for this ultra-conservative approach might be that alternate JVM implementations could in theory have well-implemented versions of deprecated methods such as the above-mentioned Thread ones.