When Star Fleet Battles was being designed back in the 70's, the source materiel used (Franz Joseph's Star Fleet Technical Manual amongst other things) indicated that the Klingons had more than just shuttles in their shuttle bays.
Specifically, they had launchers for 'nuclear warheaded drone missiles' for planetary bombardment and as secondary anti ship weapons.
But...the plans also showed lots of phasers on the Klingon ships. Phasers that were never fired in the battles in the show.
So this was rationalised as short-range phasers for anti-drone (missile) defence. Thus, the shorter ranged phaser-2. Since the Federation didn't use missiles, who was firing missiles at the Klingons?
Enter the Kzinti...
In the early years of the game, the Feds didn't have any drones, the Klingons only had phaser-2s and since drones moved more slowly than ships, the Kzinti had a hard time. Anti-drones were initially unknown, and were invented to give Klingon transport ships 'something different'. They were so good they then spread like acne.
Over time, and due to player demand, the various empires' ships and weapons evolved into what you see in the game today.