To be honest, with an integrally-suppressed firearm, I’d look for or try to derive actual data on the weapon’s muzzle velocity/energy, rather than try to base it off barrel length. The reason is that the integral suppressor, particularly with supersonic rounds, will override the effects of barrel length on the weapon’s muzzle energy.
For example, the MP5-SD is noted to drop the normally supersonic 9mm’s muzzle velocity 16%-26%, to below the speed of sound. Let’s call it 20%. Assuming we’re using the 116gr 9mm JHP, we’re talking a reduction of muzzle velocity to ~992 feet per second; from there, we can derive a muzzle energy of 344 joules, or 19 damage, a reduction of 4 points of damage from the 116gr 9mm JHP’s base of 23 damage*. Thus, you could pretty safely say the MP5-SD would take a -4 penalty to damage.
*before arbitrary cartridge adjustments.
Which weapon(s) did you have in mind?