So to preface this, I'm still a beginner (currently on my third game despite picking up the game over a year ago now...), and I turned Neinzul Rocketry Corps on for the first time this game to see what they're like. I've very quickly ran into an obnoxious pocket of space containing 4 silos that I both need to get past (Tree map; I don't have another way around) and also interact with eventually (2 A group CSGs in the area), so I really need to understand how the silos work in order to proceed.
At first glance it seems straightforward enough - "When the Silo's planet is on alert, it generates lightning or EMP warheads every quarter hour and sends them to nearby human planets." - I interpreted this as 'once the planet has been on alert for a total of 15 minutes' though I guess it could also be 'when the planet has been on alert for 15 contiguous minutes' or '15 minutes after the planet is initially put on alert regardless of alert status during the rest of those 15 minutes'.
(TL;DR of below: I try a bunch of things and can't figure out any rhyme or reason behind when silos launch)
But, well, first I briefly put the planet on alert when blowing up tachyon sentinels in the adjacent system then pulled back taking the planet off alert. Some period of time after (felt longer than 15 minutes, but I was pausing a lot to do other things so I'm not sure) I got 'warhead in x system' alerts and ate a lightning warhead. Then 15 minutes after that I got another one even though as far as I could tell the planet had not been on alert in that time at all, which made me think that maybe they get activated by their system going on alert then just launch missiles every 15 minutes for the rest of the game.
While trying to look up NRC silos in response to this I stumbled upon something saying that the tooltip saying that 1 AiP every 5 minutes being recommended is outdated and 1/30mins is actually recommended, so I started over with the same settings. This time knowing there was a silo there and having found nothing useful on the internet about them, I saved and tried experimenting.
Put silo system on alert with 2 raid starships next door, wait >30 mins - no warhead launches
Put silo system on alert with entire ~500 ship fleet next door, wait >30 mins - no warhead launches
Try to park my fleet on the silo planet - lose basically my entire fleet, but did finally see a warhead alert sometime while dealing with the reprisal waves (despite the silo system being off alert after my retreat)... which proceeded to fly into a wormhole that only leads away from my planets (and not somewhere I have scouts so I don't see what happens). Sometime later I see another warhead alert, which could have been the first one finally turning around, but the warhead's position in the system looks like it's another launch from the silo. I manage to not die to the reprisal waves & warheads, but see no further warheads (both with and without putting the system back on alert), which seems to disprove my initial 'once they're turned on they just launch for the rest of the game' theory.
Reload, blow up command station on planet adjacent to silo planet - warhead immediately launches (interesting compared to the seemingly delayed launches of the other occasions). 15 minutes later, another one. Okay sure, that seems to be functioning as I'm expecting.
Reload, try parking my fleet on silo planet again, luck out that the Reservist AI doesn't seem to want to murder me with masses of core bombers from the strategic reserve this time. Despite the planet being on very alert, the silo remains inactive until my ships get really really close then finally launches (was a reloaded save from before it ever launching one, so no 15 minute timer interfering with this one).
All in all, other than blowing up an adjacent command station being a sure-fire way to get missiled every 15 minutes I have no idea what triggers them nor what to avoid doing while trying to get past them.
In case it's relevant (I'm still entirely confused by the two launches in the initial 'way too much auto progress' iteration of this game), minor factions are
Zenith Miners 2 (reload point is ~1 hour 50 minutes, and with the internet saying these appear roughly every 4 hours these seem unlikely to be related)
Zenith Dyson Sphere 6 (It's on the other side of my space to where all this is going on, so gatlings aren't responsible)
Neinzul Rocketry Corps 2 (Finding 4 silos on the first 15 planets I explored made me wonder if even 2 was too high, though it seems to have mellowed out some since then)
Neinzul Roaming Enclaves 5 (I guess these could be responsible in some way, but putting the planet on alert by parking my fleet next door didn't trigger anything and I haven't seen any enclaves in the silo system itself.)
Spirecraft (Moderate), Botnet Golem (Moderate)
Dark Spire 4 (There are a couple of vengeance generators in the area, but they've only seen a couple of my scouts die. Unless roaming enclaves showed up to feed one, but even then simply parking fleets next door doens't seem to trigger the silos).
AI1 - 7, Reservist, Hunter 2
AI2 - 7, Support Corps/Bouncer, Hybrid Hives 2.
If you read all that, I err on the side of providing (way, way) too much detail. Sorry.