It's actually problematic gameplay-wise as well.
Effects that apply on-hit (such as gaining lightning charges) don't apply because "you're unarmed" even though the weapon is coming back (Eldrich Knight).
Effects that definitely should only apply for unarmed attacks DO apply when throwing weapons because "you're unarmed".
So I'd really like to see Larian investigate how throwing works

PS: A QoL change where Javelins and Handaxe stack would be really nice!