My 2012 only has about 65,000 miles on it, but it has been a great vehicle. Yes, it does have electric over hydraulic option on the IBC.
I also came from an 03 with the NV5600. I thought I might miss some things about the manual, but I don't.
Never have had trouble with any of the emissions equipment, but if you delete, you won't have to worry about that (although I would save everything you take off in case Pueblo ever goes to emissions testing, and for resale reasons).
I am very happy with my truck, but if I were in the market to buy used, I would agree with Chris, and would look for a 2013 or 2014 over the years you are considering. The HD's went through a significant upgrade in 2013, and it isn't just the engine/transmission options. It is the whole truck including the frame.