Yes, @Dprecated in the MC codebase can be taken as:
Modders should NEVER CALL this. But as we have not moved away from it, modders MAY need to IMPLEMENT this.
Mojang is working on cleaning up their code base a lot. So things are in flux just like every major project out there.
The annotations are a guide.
Seriously it's not a hard concept.
Are you calling a deprecated function? STOP
Are you implementing a deprecated function? Fine, just be weary it may change in future MC versions. {Just like everything else}
Remember Minecraft IS NOT a full fledged professional modder facing API. It's a decompiled internal hack of a client.
I seriously can't understand how people can't grasp this simple concept, we get FAR to many of these 'but the method is deprecated!' posts... -.-
The same thing goes for things WE in Forge deprecate. Like non-stack sensitive versions of Item functions.
You could still IMPLEMENT them and they would work fine{Because we are forced to be compatbile with vanilla}. But you should always CALL the non-deprecated form.
The only difference between Mojang's @Deprecated and ours is that we can add comments directing you to the new stuff. Mojang can't as comments don't survive the compiling process.