I've been trying to get my head around the Silthion. I'm level 235 and thus entering in their range. I've completed 1 round of the mission Aggressive Evolution and gotten the plating from the Silthion Worker. But that's where I begin to get lost.

The impression I get is that there are two separate levels to dealing with them. One involves finding the very cloaked Silthion Larva that will take me down the path of getting shiny new guns. The other is getting access to the Queen and the Hive Colony. I'm not quite ready to go for the Hybrid Larva, so my question is less about that and more about if there's anything special I'd need to do to start seeing my own Queens and Hive Colonies? I've killed a few Queens alerted to me, but never actually had one appear on my BT.

What am I missing?

you need to complete the current set of quests available to you and get to the repeatable quest at the end of the set to be able to see queens and hives of your own...

coincidentally... to be able to see the larva that starts the other set of quests, you also have to have that repeatable quest unlocked... so... just continue doing the missions

http://galaxylegion.com/wiki/index.php/Aggressive_Evolution
http://galaxylegion.com/wiki/index.php/Into_the_Expanse
http://galaxylegion.com/wiki/index.php/Controlling_the_Silthion (this one unlocks queen, hive, and larva)

Just to check, I have to have all three completions of the Aphotic mission done, but I don't actually need to have started the repeatable mission. I just need to have it unlocked right? Cause I'm pretty much right there. Just got my 2nd Aphotic planet and not far off my 3rd.

That is correct. After finishing the 3rd completion of the Aphotic mission, it will unlock ALL the Silithion NPCs for you. Queens, Hives and Larva. Well, except for the gland critter you have to hunt for the 2nd Larva mission.

Oh, I was wondering why I didn't have any Queens on my BT yet