Apologies for strayung off-topic slightly, but it's an interesting question just how much weight his rank carries. He's the ranking (Starfleet) officer of the station yes, but his actual rank was still only Commander until near the end of season 3. Would a visiting Captain be able to pull rank on Sisko? Would, say, Janeway technically outrank him?
I don't think a visiting captain could supersede Sisko's authority over station matters. Sisko's superior would be an admiral, not another commanding officer. Positionally, Sisko is equivalent at the rank of commander to any starship captain. As for his involvement in any search for a missing ship, what could he offer? Use of the Defiant? Who knows when Starfleet would get around to searching for Voyager? How many times were ships out of communications range for weeks or months at a time? Surely Starfleet doesn't get in a tizzy when a ship doesn't report immediately.
I can only speculate that DS9 wasn't considered a significant post, and there was a desire to make it seem that Starfleet was sharing control with Bajorans. On the other hand, I am surprised Sisko wasn't an admiral by the end of the series. He was heavily involved in strategy and diplomacy during the Dominion War.
Back in the 90s it might have made sense that their computers would take time to be updated with that sort of information. Even today, the most common paradigm is sharing information via some central server. But Voyager was docked at the station which had the most intelligence on the Dominion there was to have. Realistically, their computers should have synced that data automatically so it would be available as needed.
I believe the producers considered making Sisko an admiral, but thought it would take him out of the "pantheon of captains". Frankly, I think they should have anyway. They were original enough to start him out at commander, and I think it would've been cool to have a main character reach flag rank in a series rather than a movie or an alternate timeline or fantasy. Even if Voyager's computers had the latest info on the Dominion (and they had enough info to use Jem'Hadar ships in holodeck simulations) there's no reason to think the Doctor would bother knowing anything about the Dominion. Clearly the Doctor isn't completely tied to the computer, since he interacts with it by terminal rather than some kind of "mental interface".
Rank and position aren't the same thing. On TNG, Data had the position of second-officer, third in command of the ship even though Beverly outranked him. Yes, Janeway outranked Sisko, but Sisko was still the commanding officer. It's like when an admiral visits the Enterprise; Picard is still the commanding officer.
Maybe "Far Beyond the Stars" was more about Sisko's career trajectory rather than his spiritual journey: a bro' still being held back.
I don't think anyone here is arguing that it is more rational that the computer, and hence the Doctor, would not be updated with relevant information, only that is might be understandable. On the other hand, automatic updates of military and diplomatic intelligence (beyond the mere facts of the existence of the Dominion) might not necessarily be wise, expanding the possibility that such intelligence might fall into the hands of a Gul or the 24th C version of Wikileaks.
I'd like to point out, again, that the Doctor regularly interacted with the ship's computer in the exact same manner as the rest of the crew, by talking to it or typing at a computer terminal. It was clearly the case that the Doctor did not have internal access to the ship's data, despite being a program himself. It makes sense, then, that no matter how much information on the Dominion was loaded into Voyager's computers that the Doctor might not know any of it.
He must be. If he weren't, then he'd have instant recall of anything in the computer, wouldn't he? He's not just an avatar of the computer, though, he's an independent program, probably with dedicated hardware running the EMH software.
It only makes sense if the Doctor is an independent system from the computer. The EMH systems may have been retrofitted into the Intrepid-class ships, but installed during the building of Nova and Sovereign-class ships. Those EMHs may be different, and have full access to the ship's computers.
You're right, but of course from a writing and acting standpoint it does make sense. I'm not saying it was the right decision, necessarily, but it might have created more dramatic problems than it solved to have it otherwise. Oh, and... hiya, Lindley! I believe the last time I saw you was in Bethesda at a get-together. Maybe we should schedule one soon.
Given how huge the doctor's program has been established to be it's unlikely that every bit of information about current events would be periodically added to his program, unless it was medically relevant, and at the time there was no medically relevant information known about the Dominion.
1. EMH Mark II's answer was annoying to begin with. A simple "no" would have worked. 2. Even if we assume that Voyager's computer system was updated with information about the Dominion, and then assume that EMH Mark I had access to the wealth of knowledge in Voyager's database (which doesn't seem to be the case anyway) .. is it really reasonable to believe that B'Elanna would have shipped the entire library of Federation threats along with the Doctor's program over the Hirogen relay given the risk of sending just the Doctor? He also obviously couldn't pick up that information from Prometheus's database. I personally think we should take the Doctor's word for it that he never heard of the Dominion and accept that sometimes characters know less than the viewer because the viewer gets to experience everything, whereas the Doctor wasn't even turned on until the DQ. Edit to add, slightly off topic: Janeway did have another option. She and Tuvok could have sent Voyager home (The way Tuvok was talking, he could do it at a moment's notice), with the two of them remaining on board the array until the last possible second to ensure the explosives went off.
Tuvok said that it would take hours to get the Array working right. The Kazon would've returned by then.