Your arguments are really great sounding on paper. And by on paper, I mean I cant really argue with the numbers. What I can argue with is your reasoning.
Why exactly are you in nebulas? To kill starbases. There are three missions where this is not the case, and I will address each individually.
In nebulas what kills starbases the best? Plasma siege guns. Without a doubt. Second up is photon lances. Third is missile launchers. I will also explain this, now.
Spire ships have more heavy slots. Heavy slots are the only things that fit things that murder starbases. Needlers dont kill starbases very well, as you may or may not know. You may think heavy slots is a trivial thing, that youd rather have not-heavy slots, and I might address that later.
Plasma cannons, as you stated, deal 100k dps to starbases and heavy units alike. Heavy units are the most annoying of nebula ships, and often the only ones with any useful amount of hp. Dealing with those quickly is nice, because then they cant be annoying you (and it takes forever for friendlies to deal with them).
Spire lances, as per your numbers, are dealing 75k dps to everything. Feel free to quote me all sorts of 'but stuff moves'. Actually, it doesnt. The game's ai is pretty simple - Move into range. Shoot. As long as you arent moving the ship, its impossible to miss. There are plenty of targets that do a lot of sitting around - Primarily, anything in nebulas. Nebula ships in general have really high health pools, and love to sit around and get shot at. Overkill due to total beam damage isnt an issue. Overall, I have found spire lance modules to be EXCEPTIONAL at doing nebula missions.
Back on the subject of youknow, shooting starbases. I mention three missions which do not require shooting starbases.
One is the Mourners scenario. I dont actually see how there is much to discuss here - The ships that are actually a threat to the base are dealt with incredibly easily by the few alternate guns a spirehsip has at its disposal. The rest is dealing with 'fluff' medium/heavy units that just soak damage. Both plasma siege and photon lance are great here, because again - What is their ai? Fly into range of base, and then afk. Overall, not the best mission for photon lances, but not actually the worst.
The Devourer scenario is the worst, by far. It actually presents a moving target (mostly), that moves quicker than you do and has tons of hp. However, photon cannons are still the best here. Photon lances are ok, in that they still are really good if you dont happen to have zenith hull. (I really dont find the human hull worth using, with one notable pointless exception - Champion Only players with nanosubverters.) This is one of the worst missions to fail a critical gear check on, because you basically can do it or you cant. Spire ships with photon lances can do it in a pinch. Human ships usually cant (ires/polarizers notwithstanding)
And the final one, dyson things. Meh. Photon cannons do this really well. I've gotten it first so many times in my last games that I am beginning to wonder what its actual logic is. No matter, its generally easily doable with a mk1 ship *shrug*
You do mention missiles. Missiles are actually pretty good. Missiles would be great if the zenith ship had more slots, and wasnt ugly.
And finally - Your general talk seems to lead me in the direction that you havent actually tried to use a spire ship optimally. Have you tried taking a spire cruiser with plasma guns into a nebula? It ends pretty quick. A spire lance fit is slightly slower, but still gets the job done faster than a comparable zenith fits. Heavens forbid trying to use a neinzul ship for it..
How do you normally run mid-lategame missions? Do you just sit around waiting for them to complete themselves?
(the heavy beam is actually really good, but has the minor problem of being human only. Railcluster is hilariously good, but I can never seem to unlock it, and it still would have to replace a plasma gun or photon lance.)
Oh yeah, and final point - edit: redacted.