Yes! The Full elemental discharge empties all your phials and does more damage the more charges you have. Note however that there are two components to this attack: the attack itself and the phialsphial burst.
The attack itself (axe hit, cutting damage) will always deal the same damage regardless of phials used. The phial burst component will increase/decrease depending on how many phials you use.
A Super Amped Elemental Discharge will cause 3 phial bursts per 1 phial used making it the strongest phial attack of the charge blade. Although due to the long attack animation and setup time for this attack it's only recommendet to use this attack if you're 100% sure you will also land it.
Note that this only applies to the Super charge. A normal Amped Elemental Discharge (without a charged shield) will only ever consume 1 phial at a time whereas the Super (with charged shield) will consume all the remaining ones.