I don't find the scene bizarre, it makes sense given how far back in time they've traveled. Yes, Starfleet Academy is located in San Francisco, but they're from the San Francisco of 2286 -- 300 years into the future! The San Francisco of 1986 likely bears little resemblance to the San Francisco they know, aside from a few iconic landmarks scattered here and there like the Golden Gate Bridge.
Just imagine if someone who attended present-day Rockefeller University had to navigate around New York City of three centuries ago: c. 1716, long before Rockefeller University ever existed. The neighborhoods, community areas, and streets of that time period bore little resemblance to modern New York. They'd be entirely lost. And yes, they WOULDN'T know where Queens is, since the present-day boundaries of Queens was established in 1899 and it was entirely different back in 1716. Even going back to the civil war area, what is the present-day lower Manhattan commercial district and the former site of the World Trade Center was a seedy lower-class immigrant neighborhood called the "Five Points" filled with gang warfare (as seen in films like Gangs of New York).
>> Unless Alemeda gets wiped off the map at some point, annexed or renamed. <<
Given the events of Star Trek's future timeline (earth was devasted by a third world war in the mid-21st century that killed over 600 million people and wiped out most of the present-day major cities in the world -- with a handful of exceptions like London and San Francisco), I think that is likely what happened. It's probably not even called "Alemeda" anymore in the time period Chekov and Uhura are from, and may not even exist anymore. It certainly isn't used as a naval station in 23rd century, judging by their reactions. (incidentally, if you went BACK in time 300 years from the present-day, that would also be the case -- what is now Alemeda Island was originally a peninsula connected to present-day downtown Oakland, and it wasn't renamed Alemeda until 1853).
I have to vigorously disagree with this. Alameda is not some obscure spot on the map. It is an island, a city and is the premier East SF Bay county. Even if the town was renamed (or merged with Oakland at some point in the distant future, for which it would still likely would be referred to as the “Alameda” section, just as different neighborhoods in NYC retain their names), it makes no logical sense that they would not be familiar with the name, even if they didn’t happen to visit it at some point.
I think it was a bad goof by the screenwriters attempting to do a comedic scene. I was wise to it the moment I first saw it (I was 12) with the same thought, “They’ve all lived in San Francisco ! They all have apartments there. Sulu was born there. How could they not know Alameda ?” They all knew Sausalito, where the (doesn’t exist in reality) Cetacean Institute was, and that is far more obscure a place.
Remember, these are all supposed to be highly educated folks, and even if Alameda were renamed, they certainly would’ve learned that in basic geography/history or just learning about the lore of San Francisco of 20th Century yore. Add to that, when they showed the visual computer maps of the bay at SF HQ in their “present (23rd C.) day”, Alameda Island stood out on the (unlabeled) screen, which made it all the more baffling.
Maybe I make a big deal of it since #1, my father and his first wife lived there; #2, my half-sister grew up there and got married there; #3, my father was stationed there throughout the ‘60s.
They were actually asking people where the nuclear wessels were. Alameda just seemed to get worked in. There’s a couple clips on YouTube of that scene.