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I think one of the things you might be struggling with is the passive element you speak of which except for electricity, gasses, minerals (not using the hokey little harvesters) are the only thing that fill in your absence. And molds will respawn. But there is not really any system for giving a passive advantage to doing anything else.
One option is to have your traps where you have your main base and refiners. While you are hanging out doing chores the traps fill. Other than that, not so much. It's just how this game rolls. And frankly fish like everything else is just another option to make nanites and units which is dead easy. Traps and all that are just for fun. I mean what is the real use? A few nanites, some new foods that give you buffs you don't need? To fill your achievement page on fishies?
As noted above, it's a game about exploring, collecting while exploring, fishing while exploring, gathering while exploring, notating flora and fauna while exploring, maybe building a bit while exploring. Chasing ships, living ships, guns, critters, fighting pirates, tarting up your save, learning words, recipes, etc., and then restarting all over again. Don't look at it all too closely. It's just a bit of amusement to waste your spare time.
Refiners, autonomous mining units and stellar extractors are known for their forgetful inventories, which are unlikely to get fixed no matter how much we complain.
So expect the fishing traps to fall into this group of forgetful inventories, only the Deep Ore/Gas extractor and silo's correctly work in the game when your away/offline, thankfully.
I have 7 fishing bases set up, one on each biome type, each with a teleporter.
Each has 3 Auto-Traps.
I clear them all before logging off for the night.
When I log back on, I go round and clear them all again, and they've all re-filled.
During play, I do the rounds every couple of hours to re-clear them, then again at the end of my play session.
I should add, some are in Euclid, some are in Budullangr, so I'm often in a completely different Galaxy when they are passively refilling in my absence.
I still prefer to have a dozen traps with oddly placed markers than just 3 traps