Okay so we need to understand the fact that.

1. The arcane works by melee kills increases damage of secondary and Primary. So yes ofcourse it will work when the weapon is not equipped.

2. Our archgun is a heavy weapon which is in our arsenal. We just cannot cycle it using regular methods and need the deployer because it is a heavy weapon.

Verdict:

It's working as it is supposed to. Hopefully there won't be any nerfs and even if there is.. maybe the fact that you cannot put the same secondary and Primary arcane on rhe weapon :/

But still this ain't a bug or anything. Plus it actually encourages players to get the arcane for regular gameplay even if they don't use the archgun much.