Not sure if 99's were 121, would have thought 135. Shorts Sherpa's were military only and cargo. Shorts 3-30 and 3-60 (also called 330 and 360) were part 121 passenger haulers used in the U.S. They shared a common type rating and I believe that some operators used both, but I'm not sure if they were used concurrently. Though I think they must have been. They are still being used as freight haulers but there is no rear ramp. IIRC the left (port) side emergency exit was surrounded by a much larger opening that was designated as a cargo door.
Your point that there were many pax ops using unpressurized aircraft is valid. Piper even produced a turbine powered Navajo as a commuter aircraft I forget the model designation, not a commercial success. C-208 are used in short haul pax ops to this day.
As the airline jet jockeys have pointed out consumption differences between FL 360 and FL 090 may not be as much as us GA types might expect. Two factors apply. One is the fact that modern high bypass turbofan engines are just way more efficient at any altitude than the old low bypass turbojets of a bygone era and altitude just does not make as much difference as it did in the old days. The second is that below FL 100 there is a 250 KIAS speed limit so the power is likely pulled back a bit saving some jet-A.
As some have pointed out the lack of gate information and the flight number above the usual range of numbers also indicate this is a ferry flight. But without direct confirmation from Jet Blue how would you know for sure? The info we have circumstantial only.
The ability to defer (MEL) systems that effect pressurization is not uncommon. For those who have not flown with them, an MEL is a bit of a misnomer as it could be called an REL (reduced equipment list). The MEL lists what minimum equipment is required for flight AND what procedures are needed to operate the aircraft without that equipment. That is how to defer maintenance and still fly the airplane. There is also a Configuration Deviation List (CDL) that deals with missing airframe parts. Example, a gear door is removed. This will potentially effect speed limitations and climb ability. If it effects climb ability then max weight will be reduced until you get back to regulatory climb minimums.