No, you said, "food, oxygen and water are useful to the Klingons, but Starfleet does not glass entire planets just to keep the enemy from using them." If Geneva Conventions still exist in Star Trek, then that would explain why Starfleet does not glass entire planets.
First of all, the Geneva Conventions would explain why Starfleet does not destroy INHABITED planets. Asteroids, moons and comets where resources could be harvested would be fair game. But they are not in the habit of doing this either.
They HAVE shown a propensity to attack strategic targets of opportunity that the enemy needed for survival, denying them SPECIFIC resources they couldn't get otherwise. They blew up the Jem'hadar's ketrecel white storage facility, for example, and will sometimes take steps to interrupt their enemy's dilithium or fuel supplies. They would probably destroy entire worlds if they thought they could disrupt the Klingons' dilithium supply chain (and arguably DID, depending on how you interpret the destruction of Praxis between the prime and Kelvin universes). But there was nothing like that on the Shenzhou; the Klingons didn't even go there looking for dilithium, just the little box that holds the crystals in place.
Does this include the
Assault Phaser?
The first thing Kirk says when they've been discovered by Sybok's people is "phasers on stun!" so evidently, yes.
From the debate so far, it sounds like the strategic goal would be to prevent or slow down the enemy flagship's repairs in time of war
And if they had known where the enemy's flagship actually WAS, they probably would have done exactly that.
But we're talking about the Ship of the Dead, a vessel that the entire Klingon military quite literally abandoned for six months and didn't bother to come back for until somebody decided to give the cloaking device another try.
If Starfleet had any inkling whatsoever that the ship of the dead was that valuable, they would have destroyed IT, not the Shenzhou.
Additionally, why was the Sarcophagus left stranded for six months without attention from either side?
Because it wasn't a military vessel. Hell, it was barely even a combatant; apart from firing the initial salvo, the ship barely moved during the entire action and let the REST of the fleet do most of the work. I seriously doubt it would even have been a match for the Shenzhou in a straight up fight.
It was the Klingon flagship
No it was not. It didn't become the "flagship" of anything at all until Kol stole it, and then only for symbolic purposes.
Perhaps there is something else to consider.
There's nothing to consider except for the fact that the Ship of the Dead is NOT their flagship and its strategic value is miniscule AT BEST. If Kol hadn't returned to salvage the cloaking device, no one ever would have, and even if they'd made repairs and flown back to Kronos they would have spent the rest of the war cruising around trying and mostly failing to get the other great houses to take them seriously and then making excellent use of that cloaking device whenever they crossed paths with Starfleet.
Kol is single handedly the reason why the cloaking device wound up being used as a strategic weapon. If he hadn't realized its potential, the Klingons would still be using it as a "oh shit" defense system for feckless cultists.
ETA - from the actual episode:
KOL: <Beams aboarD>
VOQ: Kol, what is the reason for your welcome visit?
KOL: The last time I was hear, on the eve of the war, I hurled disrespect. Now i come with humility.
VOQ: T'Kuvma teaches that in a united Klingon empire, no one kneels but our foe.
KOL: Wise words. But words don't win wars. Your house's ship has what no one else has. Cloaking technology that can crush Starfleet. We need you back in the fight.
VOQ: We have scavenged the dead vessels floating around us in the grave yard left by our battle with Starfleet. Six months after that fight, we are almost operational again. But we still lack a dilithium processor. We are almost out of food too. But as T'Kuvma taught us, what belongs to house T'Kuvma belongs to house Kol.
KOL: May the words of your messiah, our messiah, also sustain us. Remain Klingon!
ALL: Remain Klingon!
Seems evident that Voq didn't even EXPECT to be rescued. Kol's arrival was a pleasant surprise, and he doesn't even bother asking him for a dilithium processor OR for provisions. Doing so would probably be considered a sign of weakness and/or dishonorable, hence Voq actually offers his aid to Kol as if he is in any reason to be offering help in the first place.
OTOH, everything Kol tells Voq when he arrives is basically bullshit. His real intentions are revealed later, when he points out that as soon as the war is over the Empire will fragment again. He doesn't really need the cloaking device to defeat Starfleet (or at least, he doesn't think he does, or doesn't care). He needs the cloaking device as part of a gimmick to get the other houses to fall in line behind him. Voq, Son of None, isn't going to pick up where T'Kuvma left off, and Kol figures he's going to fill the power vacuum and do it himself.
More to the point: for some reason, Shenzhou is the only ship in the entire debris field with a dilithium processor, apparently because there are no birds of prey within range of their EVA suits. Even the other abandoned Federation ships don't seem to have one, nor do the Klingon cruisers in the debris field. This leads me to wonder if maybe the Klingons need a SPECIFIC type of dilithium processor that is actually compatible with their own technology. It could easily be that Shenzhou is only valuable because it's old, while newer vessels like the Shepard or the T'plana'hath would be non-starters. That might explain why Kol didn't offer to give him a spare part. "Dilithium processors? They still
make those?"
)
