No, ablative armour is a thick skin of uh... armour...
The % is probably overall for the section of the ship mentioned, ala "Ventral ablative armour is at 50%" meaning that either only 50% of the bottom armour is left, OR it's at 50% thickness.
If Starfleet perfected nanobot tech then they could work together AS (or to move) the armour to make it a level thickness accross the board. And nanobots make their own energy in Trek.