That's a "recent" development though :) The original title back in the day were all written in assembly, you really have to squeeze out every single byte and cycle for something like Pokemon or Kirby.
Because softwares are not the only one to use cycles.
For example, in the GB, some memory space is only adressable during a few cycles, and so you have to optimize your code when you wish to update the video ram. If you miss the window, too bad.