I'm... not too sure, to be honest. Stripping the methods seems like a viable use case, but the annotation itself doesn't seem to be referenced anywhere (except for annotating things obviously). It's intended to only be used by FML/Forge and the javadocs say for modders not to use it, so I personally advocate against it. As far I'm aware, it's just a marker; FML/Forge merges the client and server and @OnlyIn is used to indicate the differences.
So it's probably safe for you to use as a marker yourself, but I'm not sure. I imagine one reason for not using it is because people might misunderstand it and somehow believe that it'll magically make certain code not run on the server/client, when it seemingly does nothing in reality.
Probably a good question for Lex or someone else who works on the lower levels of Forge, I'm curious as well.