I doubt an anti-GEF missile boat needs several dedicated anti-capship railguns.
Keep in mind that all of them but one are mounted on interchangeable mounts, so perhaps it carried something else before it could mount the railguns.
It's main gun could come in handy for shredding boarding transports and other small craft that could get in it's way, as well as disabling GEF gunboats.
Of course, it's main function would be scaring GEFs away from anything that could even possibly get such missile boat dispatched for help, I don't think that if they were indeed missile boats, they'd not fly very often due to high cost of deployment.
