This game feels just as magical as Star Trek, if not even more so.
In some ways, yes. I don't personally consider that a good reason to adopt more lazy mechanisms.
Logic shouldn't impede fun in a game. Unless it's a simulator, which Elite is not.
Elite is very much a simulator, just a rather loose one, and the world it simulates is fantasy.
Regardless, logic should always enhance a game. Plausibility and verisimilitude are important parts of immersion and benefit almost anything that isn't deliberately trying to be surrealistic.
Stealth should make sense. Whatever non-lethal approaches and mechanisms that are made available should make sense.
I would much rather have a game where I my CMDR can disable settlement sensors and communications, then convince the inhabitants to surrender peacefully through a show of force (e.g. hovering over their settlement in his Federal Corvette and knocking out all their anti-ship turrets in seconds), or provide him with what he came for ("disconnect your power regulator and deliver it, and only it, in good working order, to the SRV waiting one km due south of your settlement and I'll leave you to be rescued. Failure to comply will force us to take it and we won't be leaving anyone to rescue. I know your facility is ensured; I am taking the Bank of Zaonce's property, not yours."), than have exactly the same bland gameplay we have now, but with a magic stunner that does nothing other than add a bit of absurd handwavium to explain how it can instantly render someone insensate with perfect reliability, yet somehow have a near zero chance of maiming or killing them. Done right, it should be possible to avoid scans and thus retain a sufficient degree of plausible deniability to avoid legal (but not necessarily extra-legal) consequences.
Such options shouldn't rule out more direct ways of incapacitating people, but again, anything implemented should make sense. Remotely hacking someone's pressure suit to disable their radio and increase internal suit atmospheric pressure to make it very hard to move--with the risk of a very explosive decompression if they get shot or jostled too forcefully--could be an option. Changing the atmosphere inside a settlement to a partial pressure of O2 unable to support consciousness, but sufficient to keep most people alive, would be another--again, at some risk it takes too long (allowing alarms to be sounded) or isn't non-lethal for everyone. Hell, tackling someone then securing them with a piece of rope--or one of those twelve big spools of Flex Tape every CMDR seems to fit up their butts when looting settlements--would make more sense than 'set tasers to highly improbable and mechanistically indistinguishable!"
Of course, anything that doesn't suck would take work...which is why I don't think we're ever going to get it.