Sacred Flame PHB p.272: (Emphasis mine)
Flame-like radiance descends on a creature that you can see within range. The target must succeed on a Dexterity saving throw or take 1d8 radiant damage. The target gains no benefit from cover for this saving throw. (…)
The spell hits the target, and the cover has no effect on the attack. If an creature was using cover, and attacks were liable to hit that cover (as you said the ranged weapons would in this example), Sacred Flame would ignore the cover and potential damage to the cover.
This might be stylized as a bolt of holy fire descending from above, ignoring horizonal cover, but this does not mean the attack would be blocked from cover above either.