At 4th level you lose one spell known of your highest level. So at 4th level you will only know one 2nd level spell, at 5th only two, at 6th only three, but at 7th you will know the normal number of 2nd level spells from then on, but you'll only know one 3rd level spell. That pattern repeats as you level up, and you will finish knowing one less 6th level spell, but the full normal number of 5th, 4th, 3rd, 2nd, and 1st level spells.
Junkomancer then gives you (eventually) an extra spell known of each level and spell slot that can only be used for a junk spell. Junk spells are defined as "must be one whose Targets entry lists “at least 1 bulk of electronic material,”"
In total at level 20 you should know:
6 0 level spells
6 1st level spells +1 1st level junk spell
6 2nd level spells +1 2nd level junk spell
6 3rd level spells +1 3rd level junk spell
6 4th level spells +1 4th level junk spell
5 5th level spells +1 5th level junk spell
4 6th level spells +1 6th level junk spell
It looks like you're missing a 2nd and 6th level junk spell. You also have one too many 6th level spells.
My DM told me that by the book who my character worships limits his spell choice
This is incorrect in starfinder. By the book a technomancer can learn any spell on the technomancer spell list. Their alignment and deity do not matter. Your GM might be running a homebrew here.
Since there is already another technomancer botanist if I keep two themes I may make him a scholar in forensic medicine...
Are you referring to the generic character theme, or the game term Theme that you pick at first level? By the book you can only take one Theme, but a character might have several generic themes they follow narratively.
I wanted to use baleful polymorph on the driver of a mech suit but the dm ruled it that since I couldn't really see the driver (although I knew he was inside the suit) I couldn't target him... Is that ok? How can I use baleful polymorph against such enemies then?
If it's an actual mech, you can't target the pilot, you can only target the mech itself. Mechs are not treated as objects and have construct immunities. Those immunities don't include polymorph, so you could target the mech itself with baleful polymorph. If it's just power armor, the pilot can be targeted normally.