There is an entire section dedicated to them on the units page, but I can't seem to find if you can use them or not. I have no clue what this series is so I don't really know if you can buy one in the previous games :/
short answer: no you can not fly capships in wcsaga
long answer: first off wcsaga doesn't let you pick what you fly for a mission, and there are no capship missions included in the darkest dawn or prologue campaigns. and second the way the freespace engine works flying a capship is buggy and boring because you can't direct what your turrets shoot at and you are slow and vulnerable