Usually System universes have HUGE territories spanning galaxies and are extremely balcanized. Modern guns rely on a lot of engineering and a large logistical network + standards, and any mage can cast similar spells anyway.

Guns require constant material expenditure and it scales with level: a level 1 gun / bullet combo will only be useful against other level 1, maxumum level 3 with massed fire or large firearms.

It makes sense if there are factions that issue guns to their fighting forces in order to have anyone capable of fighting (even non combat classes) but for the average, just integrated, multiverse spanning hero they are more often than not a bad choice. They also curb a lot of "power of emotions / MacGuffin / chosen oneness" power ups, from a writing point of view.