From the patch notes:

The Aetheric Condensation of Anima Weapons

Completing duties with a sharpened anima weapon equipped will increase your anima weapon's aetheric condensation. Once the weapon's aetheric condensation reaches its highest level, the anima will be prepared to reach new heights of power. The amount your weapon's condensation increases will depend on the duty, but it is possible to obtain bonuses by fulfilling certain requirements. Players can check their weapon's aetheric condensation by using enhanced anima glass while their weapon is equipped.
So, yes, you do need it equipped to get condensation. It's pretty much a very long and special spirit binding process.