Due to relativistic corrections, E=mv2/2 actually exceeds E=mc2 at somewhere around 87% of the speed of light (the full kinetic energy equation for a fast-moving object is E=mv2/[2*SQRT(1-v2/c2)]). The chief disadvantage of particle beams is that they would lose cohesion much more rapidly than lasers and would therefore have a much shorter range. Still, by "short range," we're talking thousands of kilometers versus several light-seconds. Not really enough of a limitation to make trouble for FS2 combat.
No it doesn't. Relativistic KE pulls away from Newtonian KE pretty quickly as you get close to c. The actual formula for relativistic KE is T = mc^2/sqrt(1-(v/c)^2) - mc^2, by the way. Tell Wolfram Alpha to graph x^2/2 and 1/sqrt(1-x^2) - 1 and you'll see what I mean.
Yep, you're right, I had the equation wrong. Oops.