Paul Farquhar
Legend
If Hunter's Mark had been intended to modify the weapon's damage it would have said so in the spell description.
Compare Shillelagh: "the weapon's damage die becomes a d8. The weapon also becomes magical".
Key words: THE WEAPON.
The real unclear case is a spell that hasn't been mentioned yet: Enlarge/Reduce. The spell fluff implies that the +1d4 is a property of the enlarged weapon (and hence as magical or non-magical as the original weapon), but it actually states that is modifies the attack. In which case, RAW the +1d4 is magical even if the enlarged weapon is not.
Compare Shillelagh: "the weapon's damage die becomes a d8. The weapon also becomes magical".
Key words: THE WEAPON.
The real unclear case is a spell that hasn't been mentioned yet: Enlarge/Reduce. The spell fluff implies that the +1d4 is a property of the enlarged weapon (and hence as magical or non-magical as the original weapon), but it actually states that is modifies the attack. In which case, RAW the +1d4 is magical even if the enlarged weapon is not.