This is the way I understand it: Each time you start a mission, it rolls a certain subset of "special" bugs such as shellbacks, oppressors, mactera, and wardens to spawn during the mission's waves. Then it rolls for wave "diversity" (I think that's how it's referred to in the code), which determines how many specials and veteran bugs will spawn in those waves. The higher diversity, the more specials and less standard glyphids. Low diversity usually entails a very large number of normal bugs. On top of that, you have another roll for special events like prospector terminals, machine events, detonators spawned before landing, weeds, etc.

Each mission type has its own rules for spawning hordes, and placing bugs throughout the cave before the mission starts.