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open them, then sell the x class tech upgrades (dont open them or they lose all value)
If not, refine runaway mould, or go fishing and release the fish
here's a list of other things you can refine...
https://nomanssky.fandom.com/wiki/Nanite_Cluster#Source
You can also farm sentinels to get salvaged glass, which has a decent chance to drop tech upgrades that you can sell
They respawn not with a timer, but with traveled-from distance or teleporting back and forth between multiple base markers and/or space stations, hence "farming".
Abandoned Mode there are no NPC's/pirates so that nice option would be gone.
I think the larval cores and purple shards are the easiest things to hand-gather.
I guess I like it because I enjoy finding the critters and it is predictable and no processing required. If you are the first explorer on the planet, you also get nanites just for uploading your discoveries.
While it is timing specific, completing an expedition and returning to your regular save is the quickest way to get a boatload of nanites. Both my saves where I did an expedition with them have over 200,000 nanites after I finalized the expeditions.
Be aware that they have made gaining nanites a lot easier in recent updates, so you will be swimming in them at some point.
Once you have 3 decent scanner tech upgrades boosting scanning rewards, even if you don't finish the fauna per planet, it's stilll a decent amount of nanites re: scanning plants/fauna/minerals.
Early on, I tend to find a Sentinel Pillar on a dissonant planet and farm sentinel/purple tech, much of which refines to nanites and the suit and weapon tech upgrades sell for decent amounts.
Keep the technology you need for yourself at the start, but don't go for the best, just good enough.
Should cost you around 12 million per run and make you 10k nanites...
Anyway, it's a fast and safe conversion of units to nanites in PD mode.