Should I buy Coda 2 on the app store or directly from Panic?
As you can read on the FAQ page of Coda, there is indeed a difference:

Should I buy from you directly, or from the Mac App Store?
It's largely a matter of personal preference. Please refer to the pricing FAQ above to see which way gets you the best price.
At the moment, there is only one difference between the two versions: the Mac App Store version will support iCloud syncing of Sites and Clips, and the direct version will not. This is a restriction imposed by Apple.
Apple often changes the conditions for Mac App Store eligibility, and it's possible we may have to modify or remove features from the Mac App Store version in the future. It's our intent to keep them as close to identical as Apple will let us.

So there you have your answer.
So, if you like to sync with iCloud, you should buy from the Mac App Store.
If you like to have a 50% discount, buy from Panic directly!
I would go for the 50% discount. :)