Easily explained. A Category 9 earthquake utterly destroyed SF, and what you see in Star Trek are the replacement buildings.
Now why Starfleet would choose to build its headquarters in a location proven to be so vulnerable IS an interesting question...
Perhaps forcefields and other modern technology make buildings immune to earthquakes.
Sorry. Turns out I should have said Category 10+. A 9 appears to be insufficient to cause the total destruction required to utterly destroy SF.
The Federation is the ultimate socialist expression. Why WOULDNT they build it there?
>>Perhaps forcefields and other modern technology make buildings immune to earthquakes.
The technology that makes the Structural Integrity Field and Inertial Dampening Field would make buildings earthquake-proof.