I would be very sad if they removed the pre-firing delay from railguns. The delay makes the weapon more challenging to use, sure, but it also makes it more rewarding when you get good with it- and yes, you can get good with it. The delay always lasts the same amount of time, so once you're familiar with it, it's not that big of a deal.
What I WOULD like to see changed is perhaps a slight buff in damage, a slight increase in the amount of aim assist (making them act like fixed beams, for instance), or ideally, a rework of their damage mechanic. Even when I'm right on top of an enemy so I know I'm hitting, the railgun seems to just not do damage sometimes. Another interesting change would be for it to be capable of hitting subsystems through ships. Being able to snipe someone's powerplant from the wrong side of the ship would be sweet.
As far as a logical reason for it to have the delay, gameplay and balance aside: Heat. Something like a railgun needs a huge burst of energy to fire. The best way to get such a burst of energy would be with some sort of capacitor. Perhaps holding a charge in these capacitors would generate a ton of heat, and potentially damage the system. Keeping the gun "ready to fire" at any time would probably just consume too much power, and generate too much heat. The only way to keep things stable is to only charge the weapon when it's about to fire.