There are two kinds of militias: Confed-funded and controlled, and local militias. Confed-funded militias are the ones scanning you for contraband. The ones fighting pirates are local ones.

The Confeds are officially against the pirates, but they wouldn't try to kill their customers, would they? Nor would they have their minion militias do so. But somebody has to fight the pirates, or else they wouldn't need ships! Okay, well, let the local funded militias do so. Right? Who's paying for the local militias? Well, the confed funded militias probably have some nominal aid program by which they match any money donated privately with an equal amount on their part (of course, only the official portion of private funding); I'm just speculating. Private biz have good reasons to donate to militias… But so do the mobs, to prevent un-planned instances of law enforcement happening. That's why, probably, there are 'hunters': When something really needs to be done, forget underpaid militias with too many conflicting interests to juggle; just hire someone who will do the job single-mindedly.