thrusters are a very delicate part of a gundam, a massive shock would definatly damage them aka from a projectile hitting a thruster at crazy speeds would jumble electronics and parts. also, when kira fought forbidden in the first gundam seed, he whent right up to him and shot him with both railguns when the shield was not activated(little forbbidden deflector thing), it was a direct cockpit shot and blew forbidden back very far, however, it did no damage whatsoever i forgot what episode this was, but it was the one with justice came in to and they both fought the 3 druggies. so railguns arent completely useless against phase shift, but pretty useless( i mean freedoms head got knocked off by a mace... a physical object hit a delecate part(the head) and knocked it off. it was the sheer foce of impact and momentum, not the fact that it was energy, just like a railgun). also, railguns are NOT energy cannons, it is a graphite or metal object that is shot out very fast using magnetic fields. there is no energy involved. a huge generator is needed, but thats why freedom was nuclear powered.
"Railguns are actually relatively simple devices consisting of two parallel copper rails with a groove cut into them. A small projectile made of either aluminum, copper, or graphite is fitted in the groove. The projectile must be at least semi-conductive in order to complete the circuit. The rails are hooked up to an enormous power source which sends an electric current up one rail, through the projectile, and down the second rail. The current up and down the raill causes magnetic fields that interact with the electrons (current) moving through the projectile. This interaction is known as the Lorentz Force and acts in a direction perpendicular to the magnetic field and the current. The effect of the force acting perpendicular to the magnetic field and current causes the projectile to accelerate down the rails. Therefore, using longer rails causes the projectile to reach a higher velocity before leaving the rails, due to the fact that the Lorentz Force will be acting on a longer period of time"

now this is why its a substance gun, the projectilve moves very quicly and is charged magnetically so it gives off a weird yellow light and a laserish appearence(thats why there arent many yellow guns on seed, mostly green and red) also freedom's railguns EXTEND for the reason of of lorentz for acting on it longer, otherwise, why would it need to extend... lasers dont care about barrell length, only bullets or sum type of substance does. and also even if the railgun was substance and laser, (which it isnt but just incase) the laser would have instantly been dispersed in the water, so only the substance would hit anyways. but the thing is thet substance hit a very critcal part.