I agree, I think its a good idea to explore a relatively neglected faction.
The annoying thing is, the Hutts have always been a 3rd wheel to the conflict - yet no game has made massive use of this potential faction. If you imagine the Empire and Republic both being 40% of the map and the Cartel owning maybe 15% of the remaining 20%... they can really make a difference.
It kinda irks me they didn't include a 'freelancer' smuggler/BH that followed the Hutt side of things - the two classes have never been 100% on one side.
Concerning smuggler and bounty hunter I think its important that SWTOR, being an MMO, ascribes them to particular factions. But yes, while they often if not always side with Republic and Empire respectively, they do often work for Hutts. But like I said, they need to conform to the MMO format.
However I definitely feel a sense of independence from the Empire and the Republic in those classes. The first chapters at least are all about YOU, not the factions. And throughout the game you always side with whoever pays the most and whoever gets the most freedom and have perfectly 'freelance' motives for assisting Republic and Empire.
And personally my BH would side with the Empire over the Hutts, the Empire are more powerful and have more money, and the Hutt's a strictly neutral so my BH can work for them when he wants. Any 'rebellion' like Makeb will be swiftly put down, and more money can be gained by being on the winning side. Still, I reckon you can probably dabble with both sides when you get on the planet, but we shall see.