Well, you have to consider that most of this was filmed before they even aired the episode where JR was killed (episode 7 of the season). So, they really had no clue how all of this was going to play out with respect to the Post-Hagman ratings. I doubt they wanted to risk not telling the end of this story in case it wasn't picked up for the 3rd season (I have yet to hear an official announcement on whether or not it was, though I've seen a few outlets like tvrage insist that it has been).
The briefcase that Emma gave him? My guess would be evidence tying him to Roy and the bombing on the rig. He was arrested because they provided the police with evidence of his connection to the cartel, but there was more that they'd no doubt want to go after him for.
The only "cliffhanger" really significant enough to make people need to tune in next season is the situation with Barnes and Elena. But, if they were hedging their bets against cancellation that was to be expected. There wasn't a huge cliffhanger at the end of the first season, either, other than finding out that Pamela was Cliff's daughter.
Ultimately, they are going to have to create reasons to keep people tuning in. With Hagman gone, the ability to say "Ya gotta watch... it's Dallas" is greatly diminished. They need to come up with reasons for us to care about the younger generation.
We'll just have to wait and see.
Not sure when the next season is slated to begin.