No, cleaning it makes no difference except where the deposits cause restrictions. I suppose it could be argued that thick deposits make a small restriction anywhere for a tiny % benefit. However it may reduce the rate at which any local sensors get fouled, and of course help to make a better seal where gaskets are involved, and reduce the chance that any later (especially cleaning solvent sprayed in) dislodged chunks of deposits could make their way to valves and cylinders.
If having it apart makes a PCV valve easier to access, now might be a good time to replace that too.
As far as cleaning the upper intake, sure why not? I just wouldn't do much more than a spray cleaner, no elbow grease and scrubbing unless there's thick deposits stuck in place.