Actually, it would do something. Shields disappear during SC, but capacitors keep recharging. If you have at least 1 pip in each capacitor, then everything will be fully charged when you drop out (Including the shield).
However, if you supercruise with your shield down and 0 pip to shields, it will remain down when you leave supercruise. With even 0.5 pip, it will be fully charged during SC.
That's a huge difference. Currently, it's really a good idea to balance your pips before going into SC, because you know you won't be able to do it during SC, and it can be lethal when you finally come out of supercruise.