First part, if you are talking about the on-planet resources you can mine on colonies like those you mentioned and Harmony Crystals, Precursor Nanites they were nerfed in 2.94 and are really rare now.

If you are talking about orbital improvements like Orbital Prison, Orbital Farming, they were moved into Techs that you need to research before you can use build them. I do not know which tech as they are in various different ones now.

Cannot help you with the ship editor as I do not edit my ships just use the ones in game  

Re:  planetary resources - I'm talking about the ones you can harvest using an orbital improvement, not the ones on the surface you can unlock in a tile.  I'm also not talking about all the orbitals you unlock from techs.  Normally those resources used to be on maybe 5-10% of the planets, now it's on zero planets out of several hundred.  In the past I could check each of my planets and at least see that it had a resource like Xanthium that existed but was greyed out until I got the tech but they are missing now.  This is only a thing in 2.94 I should like to point out, it was fine (plentiful) before.  It's possible that the universe generation process on Steam Decks differ from PC, but if so it's only in this new version.

Re:  doctrine editor - I'm saying that when you edit the doctrine, it doesn't remember it.  Every time I update a ship I have to edit the doctrine and set it back to the non-default (in my case usually the -50% cooldown).  On PC it at least keeps the same doctrine settings from ship designer session to session.

I'm willing to collect more data or send in saves if that helps, but both are pretty self-explanatory.

Best regards to the team!