I think it is because your ship is still trying to engage the cruise engine, which disables your weapons. If you think about it, it makes sense. You just poured a whole bunch of power into your thrusters, and it went away to nothingness. Then, you try to put more in.....
You actually can design systems, but it's up to Igiss if it will be included in the mod (1000 mil is a bil). If it IS included, then the clan can just buy it :D.....
As for the effect for a railgun....If it goes 2000-3000 m/s, then you're barely even see the effect (if it's range is 800, it'll be there for about 2/5-4/15 of a second). You could probably just use the nomad energy blaster projectile graphic and just speed it up a whole bunch. You could also use some type of small explosion or something for the impact....
I agree with marauder on the range thing. Unlike light/whatever the weapons shoot, the railgun shoots a projectile, which doesn't dissipate/spread out and would barely slow down because of the lack of air friction (drag) (this would also apply to missiles, but that's not my point)
