I don't believe there's a "damage cap" for larger ships against smaller ships.
What I think is being referenced here is the mechanics behind weapon sizing. As you've likely seen around, smaller hardpoints do less damage against bigger ships by way of a modifier. But that isn't about nerfing small ships, or making it harder to fight big ships. By doing so they can set the damage values of large weapons only a small bit higher than the small weapons. Small weapons then do less damage to big ships because of the modifier, but when a large hardpoint is turned on an iCourier, the iCourier shouldn't get mashed in seconds by a single pulse laser because it's taking full damage from a large weapon that's only doing a bit more damage than a small/med pulse.
Otherwise to make large hardpoints have any meaning they'd have to do much, much more damage compared to a small hardpoint, with the consequence that to keep up damage against another large ship it would pulverise anything without a huge shield/hull HP.
Your clipper may be the faster killer simply because of range, as already pointed out. When you can stick on an enemy a few KM away and keep them under fire, they're normally toast in seconds.
Edit: Gimbals are indeed different across hardpoint sizes. Larger weapons track slower with gimbals. You may also have noticed that cannon projectiles travel slower the larger the hardpoint, which currently damns the C4 cannon to some extent. This was acknowledged and I believe is due a bit of a buff.