They also used plenty of Assembly programmer and special graphics units, the console percursors of GPUs.
However since the N64 that they use graphics APIs like everyone else, GBI, GX, GX2 and nowadays NVN. For porting purposes, the Switch also supports GL 4.6 and Vulkan.
Other than that, there is also a performance culture, and not using generic game engines.
These consoles - along with everything handheld up until the 3DS - create images out of scrolling layers of background tiles and freely positionable sprites. You don’t have any kind of per pixel access, although you can manipulate the state of the hardware as the screen is being drawn to get unorthodox effects.