Give the practialities of running a fleet of ships on a shoe string, I think powder powered projectiles fit the bill nicely. Railguns to my knowledge is probably going to be much more expensive than bullets propelled by gunpowder. I imagine there should be one more advantage and that would be the fact that they don't, or shouldn't, create any flux to fire. Turning the gun around remotely might take some power, or not if you have some poor sod man it outside of the hull, but the power needed to fire a weapon where the energy is stored inside of the projectile's casing itself should be minimal sompared to railguns and lasers. Much like a smaller unguided version of lasers, they really shouldn't cause much flux to be generated. These weapons are the sort where you can leave it on auto-fire to shoot down missiles and bombers and not worry about raising your flux level while the ship is direct ship to ship combat.
Hm, it is all about efficiency. I am pretty sure that the theoretical energy efficiency of a railgun should be much higher then that of powder weapons, i don't see where large energy losses would be absolutely necessary. So if you have a sufficiently efficient energy source, the fuel + bullet for a railgun should take up a lot less space then powder + bullets for a powdered gun.
However, i think one important factor should also be style. A railgun feels far "cleaner" than a powdered gun, where you are basically producing a lot of additional unwanted trash in the form of shell hulls, gases, additional heat, and so on, when compared to the railgun which basically takes a lump of metal and energy and without a lot of byproducts accelerates the bullet.
Although on the other hand you take something as complex and powerful as a railgun, they might be suited for a different purpose than shooting down small fighters or missiles. The sheer speed at which rounds can be discharged from the railgun are going to be magnitudes greater than something that has to take into consideration the expansion of gases. The ratio of space to the momentum of the shell is going to favor railguns greatly. The flux on a railgun might be incredibly high, but because of this I think such guns should be ship killing instruments or have specialized roles rather than shooting down something that a cheap battery of flak or AA fire can take down.
I don't really agree with this. If you have efficient railguns, they should be more effective then gunpowder weapons in pretty much any situation. Worst case, you need another additional reactor (or a larger one) for the additional power, but since you also need a lot less space for the bullets (you don't need bullet hulls and powder, just good shaped pieces of metal), that should balance out to still having more space left over. Also, i am pretty sure that heat, or more specifically getting rid of it, is a very important aspect in space combat. And i just can't see a railgun ever producing more excess heat than a gunpowed weapon. Sure, you have pretty high currents to induct the necessary magnetic fields, but as long as you have good enough conductors that should still work out. Using superconductors might be problematic because of the formerly mentioned heat problems, but it is pretty easy to increase the conductivity of any conductor by simply increasing its size.
Though you might have a case if for some reason it is only possible to build effective railguns from a certain size upwards.