It's always the amount of coin. Well let's see, you get 500 either way, so it's a mysterious case indeed, BUT... Kematu said he gives you half of the bounty, that means the actual bounty was 1000, while if you chose to help Saadia she gives you only 500 for saving her life. 500 coins for your life, seriously?! I mean did she even consider I had the option to betray her?! Case would be solved, BUT... we shouldn't forget that she works as a barmaid so probably she gave you more than enough coins in that occasion. The only thing that bothers me that she didn't say anything like "Oh thank you for saving my life, if I ever get back to Hammerfell you are more than welcome at my place at anytime because I am a noble and my family is going to be so thankful for saving me that they will make you swim in sweetrolls" or something like those original "thank you" lines. Everyone has to admit that she could have said something like that at least, that's a little fishy.
OK let's talk about Kematu. As I mentioned he says he gives you half of the bounty if you help him track down Saadia. We get 500 from him if we do so, that means the full bounty was 1000. But how do we now he did not lie? I mean we never saw the bounty for Saadia, we don't know how many coins we should get. What if Kematu gave us a lot less than we deserved?! The cheap bastard. But OK, let's say he gave us the deserved amount. That means Saadia has a high bounty on her, but is it high enough for someone who gave away a whole city? That would be 1000 coins, yeah right. So either way he cut our payment or he's not telling the truth. Same for Saadia. At least she could have said she's going to send the other half of our payment if she ever gets back to Hammerfell. With a courier. Oh wait that courier would actually get more coin than us, making his way from Hammerfell to Skyrim.
Actually I am very bad at conclusions, I just thought I'm going to point those things out, maybe there is someone who is smarter than me. In my opinion even Bethesda wouldn't know the answer.
(Someone mentioned they were attacked by the Thalmor Execution Squad after helping Kematu. Or was it Saadia? Nevermind, because b*tch please, I ran into them when I was level 3, haven't finished any quests at all and they still wanted to kill me! Where is your God now?)