I think it would. My understanding of that would be that the armor adds to the penalty from Dim Light and Total Darkness. Partial Light and Full Light do not get the beenfit from the mod. Since Low-Light Vision says "Treat Partial Light and Dim Light as Full Light", it wouldn't affect someone with that trait.
Also, in my games at least, those kinds of mods are applied to the armor and I just have them affect the helmet too, though I don't allow normal armor mods (like Nonconductivity or Thermal Dampening) on helmets or other armor accessories. That way there's no confusion on what stacks and it stops dumb things like having shock weave on your helmet, or having to pay the exact same amount to get ruthenium on "everywhere but my head" as "only my head". It's probably not how it's intended to work, but it needs errata. Some GMs might say it's not possible, for instance, to have body armor that counts as "almost full" and then to combine it with a helmet with the coating.