That's the main difference between hit-scan and projectile weapons.

Even now, most games that use modern-day weapons alongside fanciful ones do this. I guess cause it's easier to program guns that way, especially since one can't normally see bullets in real time, but energy weapons can be detected by the naked eye.

Also, we expect energy weapons to have visible projectiles. This is know in TV Tropes parlance as The Coconut Effect.