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They can remove them, though?

Like deactivated firearms?

Even if we assumed that passangers were allowed everywhere on the ship, something that not even civilian ships today allow, removing the internal workings from a phaser shouldn't that hard and torpedo lauchers can simply left unloaded (and if you want be extra sure just remove enough stuff that they look right but won't funtion) kind of like WW2 era planes flown in airshows are probably not only loading the right kind of ammo away from being turned back into fully funtional warplanes.

That's exactly what happens to the E-A in the first shatner verse book. They strip all the weapons, classified materials and sell it an Ambassador as a private yacht said Ambassador is Kirk's new girl and gives it straight back to him but its a plot point they have to shove klingon disruptors in it for weapons.

In the old FASA Star Trek series, they explained things this way;

When the Enterprise-Nil went in for refit (between TOS + Movie 1), in addition to the upgrades, Scotty suggested a few more changes that resulted in the visual differences between TOS + the movie. So Starfleet switched all Constitution production to the Enterprises-Nil's new specs, and named the ship class 'Enterprise'.

They also had several other ships do the same thing (one of them being the Reliant)

Prometheus Unbound wrote:
IMO it's either the Yorktown, or it was meant as a new / reconditioned ship that got renamed at the last minute.

... Or no, thinking about it, Ent-nil was due to be decomissioned.. but then the crew was being reassigned .. I don't think it was originally meant to be The Enterprise when it started construction, whatever its origin.

The Enterprise was being decommissioned because she was "20 years old", and also pretty wrecked from Kahn's attack. They mentioned there were twelve constitution class starships in the original series, I remember the constellation, the potempkin, the hood, the exeter, the defiant, intrepid, lexington and excalibur, and presumably there was a constitution, the class was named for, although if you believe the book Final Frontier, the Enterprise actually WAS the first, and some naming, production snafu made it 1701 and enterprise. Either way there 9 or 10 named.

I never understood the 20 years old comment though, April did a 5 year mission, Pike did a 5 year mission, Kirk did a 5 year mission so 15 years, than apparently 5 years from Kirk's first mission, to the time of TWOK? I mean maybe, if they started the refit right after Kirk was promoted, and it took a year or two, and TWOK was a year or two after that, but I got the impression more time had elapsed. Either way, if the Enterpise was 10 when Kirk took command, they could have still been finishing the first 12 ships, so the last few might have been only ten years or so old when TWOK took place. The series didn't even mention them all, which would make sense in universe if they were still just being launched and weren't well known yet in the fleet when the Enterprise left.

I particularly like the idea that the Yorktown was one of the unmentioned ones, and the probe didn't cause as much physical damage as Kahn did so they just gave it some internal cosmetic renovation and sent it back out. If it had already been refit, and they took that kind of shortcut, than maybe the probe screwed up all it's systems and Scotty was grumping about getting them back together. I DON'T think they would give Captain Kirk a ghost ship, and he didn't really have a crew any more, just a command staff so they could have just given him the ship and it's crew, and sent the other command crew elsewhere.

The Exeter was left floating around whatever that planet was when it's crew all got wiped out though, so if they ARE handing out haunted starships, it could have easily been that.

There's a fan/novel theory that Kirk did a second five year mission in between TMP and TWOK, iirc. That would bring it up to at least twenty and if we assume the Admiral was being approximate rather than exact, there's plenty of wiggle room for refits, shakedown cruises and time as a training vessel to make a bit more or less than twenty years (depending if you buy Kirk's 2nd mission or not)

That's not really a fan theory though, as IIRC that's exactly what 'Star Trek Phase II' was going to be-- another five year mission. Its flop meant that they went straight to TMP, and how that went, well.