You're right that there's something funny about +% cards, but you've got the details wrong.
In Renewal:
+% damage vs monsters of race/element/size (including +% atk effects) effect only damage contributed by WATK and EATK not SATK. (see http://irowiki.org/wiki/ATK for details on what those mean).
Damage modifiers for weapon element work much the same way (however, weapon element from Mild Wind, which is autocast by some of the zodiac hats, does work on the whole damage)
+% damage with ranged attack, and +% damage with a specific skill type effects work on the whole damage.
In Classic:
All +% damage effects, as well as weapon element, apply to the whole damage.
Edited by DrAzzy, 09 July 2014 - 06:57 AM.