If Drach’Nyen exiles a commander and it’s put within the command zone, Drach’Nyen doesn’t give any bonus energy.

Drach’Nyen’s second capability says

Equipped creature has menace and will get +X/+0, the place X is the exiled card’s energy.

The phrase “the exiled card” can solely seek advice from a card within the exile zone. If the cardboard just isn’t within the exile zone, that a part of the power doesn’t work. This is laid out in rule 607.2a:

If an object has an activated or triggered capability printed on it that instructs a participant to exile a number of playing cards and a capability printed on it that refers both to “the exiled cards” or to playing cards “exiled with [this object],” these skills are linked. The second capability refers solely to playing cards within the exile zone that have been put there on account of an instruction to exile them within the first capability.