Check out the patch notes for the v18 Kritias Expansion here: http://forums.maplestory2.nexon.net/discussion/45974
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no. Whether the damage is magic or physical has no relation to whether it's elemental or not.
To be clear, runeblades do both physical and magic damage, but we usually do more physical damage. Whirling blades and echoing blades are both purely physical.. with rune they might do physical fire damage, physical electric damage, or physical cold damage, but it's all physical.
Illusory blades does magic damage with no elemental sub-type. Warding rune is pure magic, but can be magic fire, magic cold, or magic electric. (well actually the cold version doesn't do damage.)
Some other abilities do physical damage on the initial hit, and magic damage on secondary hits.