Remember, science is not meant to be holding up us veteran players, its to slow down the information overload for new players, so yes, you can game the system in ways new players wont be able to, but thats not a bug.
I guess that will be up to the modders as to how they fit in with the tech tree... In Sandbox they will still be available for normal use, and I'm sure hacks will spring up in no time.
There is no situation that makes everyone happy unfortunately.. If no announcement is made, then the forums fill up with complaints about that after the release. Such is life.