If one faction eliminates other, will they acquire their blueprints and maybe start producing their ships? Is there an option to make so factions cannot be eliminated without significant player's involvement? Or at least give a huge warning about such possibility? Because I was just doing stuff, making money to finally buy some nice ships, when Diable Avionics just eradicated Spindle. I know I can resurrect them by giving my colony, but it's a chore. And I guess their leaders and missions are gone anyway?
No blueprint "inheritance". As for how to prevent faction elimination, well, there's a few things you can do. You can decrease the invasion fleets strength in the config/lunalib settings (and decrease their frequency). That can make it much less likely for invasions to reach the target market. In theory, this should be especially true for small factions like Spindle, or Mayasura, who tend to have a lot of defensive forces all concentrated in one spot. But if those forces are otherwise occupied when the invasion fleet arrives (for instance, an unrelated pirate raid going on), then it might still reach the planet and at that point it's a toss of the dice.
In the settings you can also specify a grace period from game start before the invasion logic kicks in: by default it's 270 days iirc (which isn't a lot), you could also increase that to give you enough time to build yourself up before things heat up in the sector. Perhaps even better, if you don't start as an already established player faction, you can set Nex to ignore invasion logic until you have founded your first colony. It's what I do nowadays: this lets me take my sweet time doing early-to-mid game stuff, and when I feel like I'm ready - and willing - to personally intervene in a more chaotic 4x environment, I create my faction and let things explode.
BTW, there's also a setting at game start to allow faction respawning. Basically after being wiped out they can respawn with an invasion fleet and, if they win, get back in the game. It's a bit random and not often very successful though (even if they win the invasion, they then tend to be killed again soon after), and yeah, any custom npc and related mission that got previously wiped ain't gonna come back.
By default, Nex is setup to be VERY chaotic and fast developing (especially if you've got quite a few modded factions in, it gets messy quick). If you are a player who wants to take things slow, you may want to mess with all the aforementioned settings (and a few others too, like the frequency of diplomatic events that can lead factions to war) to lower the overall 4x pace in the mod.