Too Much Datamining - We all know what will happen. Someone will datamine and hack the game files and then before you know it, the Thargoid homeworld, Raxxla would be exposed and you could forget putting anything nice in the game because it would just get hacked out and the game would be ruined again.
I watched as a small group of players ripped through the 'mystery' surrounding the Thargoids, the barnacles, the encoded messages, and so on, and posted all their findings on YouTube. I'm sure they had great fun working it all out, but it didn't leave much for the rest of us to do once they'd finished. All we needed to do was go look up their videos and all the mystery went away.
(And then we had extra alien pew-pew, so it was all worthwhile.)
The point is, what you fear, and advance here as a primary reason ED shouldn't have been single-player, is basically "spoilers". But certainly to me, and I'd suspect to other non-hardcore players who might be just as unlikely to get in on that sweet, one-time codebreaking action (no pun intended) in the few days or weeks it's presented to us, it doesn't really make much difference if those spoilers come from hackers or just very clever people swarming all over the puzzle and working it out in a matter of hours.
So, sure: if you put cleverly hidden secrets in the game, then multiplayer or single-player, someone's going to expose them, and then it's up to you to decide whether to go look at their exposés. I don't see that it really makes much difference who's doing the exposing.
On the other hand, if you've created a fulfilling and entertaining game, in its own right, independent of any little Easter eggs or other nuggets you might hide in there, then that potential for exposure becomes less of an issue.
OP, I pondered a bit and imagined Elite being single player only from the get go. I made myself sad. I wouldn't know the wonders of ED's galaxy or have any drive to care about it. I imagined a world in which I had no idea about Raxxla, the PF's motives, and player faction politics.
I find this argument absolutely bewildering. "I can't possibly enjoy a game if it's single-player because I can't care about it." Maybe you need to have been brought up with multiplayer games as the norm; but as a certified Old Git®, I can promise you it is perfectly possible to care about a game - even a game world - without a multiplayer option.
I get that 'mod extend the lifespan of a game' retoric. It's not like Elite's dying as is. Good games last forever... (Armored Core, Battlefield, BlOps, Worms, Frontier Elite...)
Yes, good games last forever (until they stop lasting, anyway). And you've listed some (though I've no idea what that one in the middle of the list is). But only time will tell whether ED can stand among them. The "mods extend lifespan" 'rhetoric', as you call it, is simple logic. The ability to mod a game gives that game another way to evolve, which can help it stave off stagnation and hold its community's interest long after the developers have lost theirs.