Dwarf Fortress is a single threaded application. It is also very memory intensive. Also, it is not a 3D program. 3D applications can offload a lot of graphics processing to the card, 2D applications can't really, they need to generate the image in memory and then transmit it to the card. But DF needs to be using its memory bandwidth for its own purposes. And the constant bit shuffling means you will be suffering cache misses, where the processor has to grab data from slower main memory, much more frequently.
The FPS cap is for the world simulation frames per second. The graphics FPS cap is for how often the picture of the world gets updated and sent to your GPU. The processes of updating the world and udpating the graphical picture of the world are in direct competition for your computer's scarce resources. Because this is not a fast action game, you don't need to update the picture of the world as frequently. It won't look any more jumpy or jerky than it already does!
By "open areas" I don't mean they are open at the edges, I mean they are open in the middle. Because of the way that computers figure out the way from point A to point B (an algorithm called A+ or A*) having many equally valid paths from any point A to any point B means more possible paths to check. Do I go north, then east, then up; or do I go up, then east, then north, or do I go... you get the picture? More ways to go means more ways to check, conversely, more restrictions on travel means less paths to check, every millisecond, for every creature.
You'd get better FPS from a 3x3 or even 4x4 embark that didn't have all those mined out areas. However, you can fix it easily, after you get what you want, shut off the access. A locked door or constructed wall in the right place will block the pathfinding algorithm, meaning it has less work to do. If your dwarves no longer need to get somewhere, make sure they can't or they will constantly be wondering if they should, via the pathfinding algorithm.