Hi CCMuffins,
I, also, am a huge nerd (not physically speaking though). I play several d20-based and RPG-style games as well as tabletop homebrews and have run into exactly what you are asking about. I find that, generally speaking, using names or ideas from other series' or fandoms can be fun but it can distract from what you are trying to create.
For instance, I enjoy Lovecraft and have named several oceans some form of "R'lyeh." Whenever I do this I enjoy the nod that I am making to my inspiration, but what inevitably happens is a player or spectator becomes aware that a quest associated with this place will be Lovecraftian in nature or have the system's version of Lovecraftian. This is why I think it is a double-edged sword.
In the first place it is nice to have inside concepts and references to make among friends. This reinforces your group identity and makes you feel safe and connected to them. However, in the second instance, you are being somewhat lazy in relying on your references to build a sense of place or a feeling about a particular landmark. I am not trying to be preachy, I also fail sometimes and am very lazy most of the time. But if you can take the initial idea or inspiration that comes from a reference you want to make or a name that you would like to use and then BUILD off of that idea into your own concept and feel, that is where you actually want to be. Because then, your world is truly yours and while you can list influences and inspirations, the content was created by you.
All of this is to say I think using referential names in map-making (and gaming in general) is like playing with lit dynamite. It can go off in your hand and ruin your day, or it can blow a hole in that mountain and make your day way easier. Overall, I'm not going to judge you if you named some stuff on your map after things you like. We all do similar things, and I would like to see your map anyway.