The active stacks are reduced below the turret count if a turret is destroyed with D when there are more than 3 turrets.
E.g. You can have 4 turrets (3 stacks) destroy one and go to 3 (2 stacks).
You have the wrong talent in the title. It should say “Overcharged Capacitors” instead of Overklock.
I confirmed in Try Mode and an AI game that yes, when a turret is destroyed it is always decrementing the stack count, even when the resulting turret count is still >= 3.