Do not read this is you're going to play Long Arm of the Hutt as one of the PCs.

We're soon through the first act of LAotH. So soon this Ota NPC is going to show up. But there's now explanation to whom he works for, why does he want to help the PCs and what's in it for him? I gather that he is trying to make Teemo's life difficult, but why? He is very helpful, but how does he know that going to Piddocks party will help PCs with their bounty against Teemo?

I'm thinking of giving him some other motive which the PCs should use as secondary objective in the party. How did you play this out?

The adventure is left vague on that point. On page 28 when asked if he's part of the Rebel Alliance he answers "Of course not." You could make that into a sly fib on this part as he is seeking guns for the Rebels and to put an end to a Hutt who is proven to work with the Empire.

Also, if you want to generate some long lasting connections you could make him an agent of Black Sun or a rival Hutt. Therefore if the party takes down Teemo Ota's master will seek out the heroes again for further "opportunities."

Just some thoughts.

I'm gong to make a table and roll randomly to determine who he really works for

The obvious (most likely given the EU) answer He's a member of the bothan spynet and the bothan spynet either has their own reason for wanting teemo out of the picture or that would help one of their allies/assets (trading favors) that maybe the twileks in the story (ryl and having twilek agents would be eminently useful to the spynet, it's a stereotype but everyone expects any bothan they meet to be a member of the spynet, so they need agents of other races). And seriously what did Ota give them other than information? No money, no gear, no transportation, no direct assistance, no risk... he's getting the pc's to risk their lives to do a job for him (that he can trade for a valuable favor to be named later), and he's not even going to pay the pc's to do it (note that the money he offered was teemo's money that was the bounty on the pc's). I think that is perfectly in keeping with the bothan spy net's standard operating procedures.