There's not any reason to think that the AP1 alters the way the Thunderhammer works, aside from the +1 to penetrate. It's just an additional effect that GW decided to slap on.
Chaos Codex
"Daemon Sword Drach'nyen and Talon of Horus
...The effect of these two powerful artefacts means that Abaddon counts as equipped with a Daemon Weapon that doubles his Strength (to Strength 8, as shown in his profile) instead of the normal +1, and he may re-roll any failed rolls to wound in close combat."
Who the heck spells artifact as artefact? Frickin' British English.