Well, this is how it has always worked and was intended as far as I know. For Cycles I decided to use viewport visibility by default and add an option to use render visibility by selecting to render according to the active render layer. But there is no such option for Blender Internal and I don't want to spend the time to implement it.

I can easily change it to always use viewport visibility but I don't know if that's better.

If changing it means to use the eye icon for viewport while the camera icon works for rendering (F12) then that is fine.
I hope this won't affect baking since it uses the Render icon as well afaik.

Oh, so there is just one option for BI..
Then just leave it like this..It would be even more confusing for rendering.
Too bad. Once Cycles supports baking it would not matter anyway.

No, it's about what's best for some people's workflow, some might want to see render visibility in the viewport and others viewport visibility. Anyway I changed it now to use viewport visibility, we'll see if someone complains about this because their workflow relied on it.

Viewport visibility is used to optimize viewport performance on heavy scenes. Same idea is used on the modifiers.
So now it will render (F12) what is visible in the viewport !? Or this just affects rendered mode ?

It only affects viewport rendered draw mode.

Committed d81f492d08e6 to bring back the previous behavior that rendered viewport always uses render visibility, because 162d6c73e3d0 caused some problems. For example, mesh deform cage is drawn as a solid/textured mesh (not a wireframe mesh) and its unnecessary surfaces and shadows mess up the preview.

We need more discussion about the way to take viewport visibility into account.

I find it confusing that object visibility in the viewport rendering behaves different to the real rendering.
In my opinion it would make much more sense if object visibility would behave the same in viewport and final rendering.