I can not really decide which one I prefer, because these two classes, Musketeer and Cannoneer, are so different from each other and have specialty on their own aspects.
Musketeer is good for PvP and attacking single target. Out of the six Musketeer’s skills, only two (Covering Fire and Penetration Shot) are for AoE, but as Multi Shot, Covering Fire is way stronger when you use it on a boss or elite monster. Bayonet Thrust and Butt Stroke are apparently skills for PvP use. The other two skills, Head Shot and Snipe, are one shot skills that deal single high damage on one target alone, which are more useful on PvP as well, when you hide far away on that back line and to the enemies’ surprise attack them out of no where.
While Cannoneer is, on the contrary, excellent in PvE and multiple targets. All of Cannoneer’s skills are AoE and deal pretty good damage. Moreover, there must be a place for Cannoneer in guild war, which is likely to be added in the future, since Siege Burst deals five times damage on enemy’s structures. However, one flaw in this class is that the animation delay of skills is quite long, compared to that of Musketeer’s skills.
Therefore, I would not say which one is stronger. Which is more suitable for you just depends on each class build you choose.
As for the damage, I think it is because of the fact that there’s no proper weapon (cannon and musket) for these two classes now. Musketeers and Cannoneers at present can only wield those mediocre weapons that NPC gave when enclassing. I believe when some higher grade weapons are added, we will eventually see the true damage that these two classes are supposed to perform.