The Hammer of Thunderbolts has a special thrown property:
The hammer also has 5 charges. While attuned to it, you can expend 1 charge and make a ranged weapon attack with the hammer, hurling it as if it had the thrown property with a normal range of 20 feet and a long range of 60 feet. If the attack hits, the hammer unleashes a thunderclap audible out to 300 feet. The target and every creature within 30 feet of it must succeed on a DC 17 Constitution saving throw or be stunned until the end of your next turn. The hammer regains 1d4 + 1 expended charges daily at dawn.
I suspect it is probably the case, but just to be sure:
Does the special thrown attack of a Hammer of Thunderbolts deal damage, in addition to its stated effect? (2d6+1 + Strength modifier + other bonuses if any)
In the Making an Attack section of the Player's Handbook (p. 194) the process for making an attack is as follows (emphasis mine):
Since the the Hammer of Thunderbolts doesn't specify that its thunderclap replaces the weapon damage, the thrown attack does regular damage in addition to the thunderclap effect.