Weakness and Resistance are not applied. Night Attack doesn't do any damage at all, and Weakness and Resistance are only factored in when an atack does damage.. You are "placing damage counters" on the Pokemon of your choice, which is not the same as actually doing damage. This effect goes through things that would otherwise prevent damage, such as Pyroar FLF's Intimidating Mane Ability (But not Suicune PLB and Sigilyph DRX's Safeguard, because they prevent all effects of attacks, not just damage). It's also not affected by things that would boost or reduce damage, like Muscle Band or Hard Charm.