First of all, I think one must define the term 'shooter game.' Obviously, you are talking about a game that has a first-person perspective, but within that you have a wide number of variations, such as action, adventure, rpg, or a mix of such elements. For the purposes of this response, I am going to focus on first-person perspective titles which involve shooting, but may also include other types of gameplay.

There where quite a few first-person games that implemented real-world locations prior to Duke Nukem 3D. One of these was The Terminator, which was released in 1991:

https://www.mobygames.com/game/terminator

Based on the movie, The Terminator was set in fully 3D modelled Los Angeles. The game allowed you to play as either Kyle Reese or the T-800, and you could drive cars, shoot people, shop in stores, walk around, and generally enjoy yourself in an open-world.

Another game that was set in 'real life' (though in the near future), was TekWar:

https://www.mobygames.com/game/william-shatners-tekwar

This game included environments such as cities, subways, and apartments, and also had non-hostile NPCs. Having played the game growing up, I can testify that in no way should it be called 'successful', though.

This should demonstrate that it was certainly possible to portray real-world locations, but I believe the reason this was not widely done was because of the nature of the market. Games set in science-fiction, pulp, or horror environments were simply more popular. It was Wolfenstein and then Doom (both released by ID Software) which popularized the FPS genre, and these games had things like Nazi-zombies, demons, hand-held miniguns, cyborgs, and energy weapons. Games released by other companies would follow this formula. Star Wars: Dark Forces, Terminator: Future Shock, Rise of the Triad, and others simply catered to what settings were popular at the time.