A dev once said, long ago, that "all the permits are there for a reason". Of course, most of the dev team that was around when that was said are no longer around, so I suspect that the original "permit master plan", if there was such a cohesive document, is now out the window.
That being said, the currently-existing permits that apparently "do nothing" do make for a handy receptacle for "future content" when the future eventually arrives. The Sirius permit used to be completely pointless, and only the diehard permit collectors obtained one. Then it became a must-have permit for the min-maxers to attain perfect engineering, when they decided to put a crucial access-controlling Engineer in Sirius. Now, everybody eventually gets a Sirius permit, whether they like it or not.
As for what's "worth getting", it depends on your playstyle. The gotta-engineer-everything crowd "need" Alioth and Sirius. Rare Goods collectors need" places like Crom and Jotun. Ship-unlockers get the rank-locked permits like Beta Hydri and Summerland, whether they want them or not. Want to buy an Orca or an Asp Explorer, cheap? Go to Alioth, for the cheapest ship discounts in the game (but only for those two specific ship types). Some, like Isinor, seem to have some kind of strange story-arc aspect to them. And others have nothing at all, except for those few who have set themselves a goal of "getting all the permits".
Finally, of course, are all the permits scattered about the galaxy that no-one has ever discovered how to unlock. Are they simply permanently locked out for reasons best described as "laziness", or is there some arcane mystery to solve that grants you one of those super-secret-mystery permits? There could be anything, from Raxxla to friendly aliens, behind those permit-locks. Few tinfoil-hatters are unaware of the mystery of these lost permits.