If you are that worried about keeping your effect systems running on your ship why are you using logic in the first place? They offer no combat benefits unless used as logic heat seekers. Also the fact that logic blocks weigh less than other blocks adding them to your ship in place of hull or shields will actually make it easier to maintain effects not harder, unless you replace the effect modules yourself which is more user error.
Routing wires through floors, walls, ceilings and even designated maintenance areas is an already possible, perfectly acceptable method of hiding wires.
There are still quite a few effects that are based on block count not mass, as well as a few more block on the inside, often means more space needed in the hull armor. I do not build doomcubes, doombricks, or a "combat ship" with a armored core room and nothing but systems and weapons.
I accept that making a ship look good inside and outside will mean having "combat useless" blocks. That does not mean I should waste even more block space on something that is always shown with no options of control.
Having "routing wires" being a common thing is alone enough to prove why its not "acceptable". These are actions people have gotten so accustomed to they think they are fine, when all it takes is an option we should already have to fix it all.
Logic pipes in large numbers cause huge FPS loss, even when none of them are "shown", sections of some of my large logic system bring me down from 120 fps to 3-7.
Your latest points have really had no effect on convincing me against how I feel about them.
