Well, in the case of Barnegat Branch, even if they wanted to run trains there again, the TRIT is pretty much gone and NJT probably wouldn't want to run along the FIT and SOUS as long as freight is going there.
Whereas with the Seashore Branch, it connects directly to an NJT route. The Henry Hudson Trail is still owned by NJT/NJDOT, iirc.
In addition, I know the Henry Hudson Trail in northern Monmouth County has a lot of crime issues. I won't lie, back in high school, some friends and I would back there to do things our parents wouldn't let us do in the house (
), and we saw a fair amount of dopeheads and methheads shooting up there. I've heard from some of my EMT friends in Ocean County that the Barnegat Branch Trail has similar issues the closer you get to South Toms River.
Not sure what the popularity of the HHT up by Highlands is, or how much it is used. All I know is people complain about drifters there often. The Henry Hudson Trail through Marlboro etc. is extremely popular and the local citizens with much money threw a fit when MOM was happening and they tried ripping the trail up to put tracks down