The obvious solution to make pirates more than just filler enemies is simple. First, give the chosen pirate band a remote and very inaccessible base, i.e. a nebula. Sure, the GTVA might have the manpower to station a destroyer in the nebula, but if it plays havoc with sensors and comms, freighters are pretty helpless when traveling through without an escort.
Next, make the pirates a bit more intelligent. If we're to believe that some of these folks are ex military, they're not going to blindly attack anything that moves. They'll pick and choose their targets, striking low priority or unescorted transports rather than attacking huge convoys. Granted, they'll attack them if they feel they have the element of surprise.
And finally, give the poor guys a backstory for pete's sake. As we can plainly see, piracy isn't all that easy, so why do they choose to do it? Maybe they're fed up with trying to make an honest living and are going for the quick and easy route. Maybe they're bitter at society. Who knows, but at least mention something about it.