Thats the point. Especially because some pirate bases pirates can cause immediately a 50 % accessibility loss and luddics can disrupt industries for 100+ days.
And they bypass colony defenses too, unlike invasions from major factions. This is why I consider Pirates and Pathers the most important endgame enemies, and loadouts that are not very effective against major factions (like beam boats) are more useful for this release. I suppose Remnants can be important too if player wants their loot.
With current skills and bugged nanoforges, it is possible for player to meet demand and avoid Pather cells. For next release, changed Industrial Planning 1 means player will need items (cores or synchrotron/nanoforge) to satisfy demand for some of the more useful industries, which means Pather cells will be unavoidable. Actually, if I want to build pristine ships, then pathers will already be unavoidable after that nanoforge bug gets fixed next release.
One problem with a big empire with built-up planets scattered around is pather cells. If I need to kill more than one pather base to defend my colonies, then the time wasted on babysitting increases, possibly to unacceptable levels. The yearly quota for babysitting required to defend against pop-up pirate activity and yearly pather purge is already obnoxious. There needs to be a way to pay bounties or commission NPCs to kill bases when colony threat alerts flash at the worst possible time (e.g., halfway between your colony at one sector fringe to red planet or tech cache at the other side of the sector).
And next release, when defending against invasions will cost reputation, player will probably need to take time off (from fun stuff) to repair reputation from time to time.