The Mods/Enhancements/Augments will have the same effectiveness no matter the armor type (L/M/H/A). Armoring stat boosts will also be unchanged. However, Armorings have a set effectiveness that is modified by armor type (so an armoring of a certain level will give a better damage reduction for Medium armor than Light armor).
In short: Your mods will have the same effectiveness in any moddable armor, but weaker armor types give less damage reduction. (In addition, some weaker armors need to be repaired more often for more money.) That said, after a certain point you can get away with weaker armor types as long as you keep your mods up-to-date.