I have a few rails with 55% heat bonus (long range), so it does cut both ways, they haven't been nerfed to 40%.
@Aashenfox
You sure that's not the dodgy UI maths, which used to express (/overstate) the reduction?
The current rail special reduction drops the thermal load on a c2 from 20.0 to 12.0.
What's the thermal load on your legacies..?
@Tandko
Frontier's reason is that the new -40% on rails is intended to achieve rough parity with the best secondaries on legacy mods.
Whenever they change the actual values of a mod or weapon, it's retrospective. So the plasma slug (slight) buff was retrospective and HYS buff (tightening of damage sphere) and nerf (damage) were retrospective.
In other words the discrepancy you identify is between changes aimed at specials/weapons themselves and changes aimed at grandfathering and secondaries.
(Not saying it's right, just saying it's Frontier's reason.)