This info may be a little out of date, updated information will be greatly appreciated.
I was a train dispatcher trainee on the NJT ML/BC/PVL/ST desk during most of 2002. We dispatched the Southern Tier (ST) between Suffern, NY and Port Jervis, NY. At that time there were 2 locals that ran out of C.H. Daytime it was HO-8. HO-8 ran east from C.H. as far as Harriman, NY. The primary customer there was Napera Chemical. There was no freight service between Harriman and Suffern. H-55/H-56 were based in Suffern, NY and worked from Suffern east. HO-8 would also run west from C.H. to 4 Story Jct. and down into Middletown. I'm not sure what customers were served, but NS (CR) also interchanged with the Middletown & NJ RR. On occasion HO-8 would go all the way to Port Jervis if there was work there to be done. In regard to the Hudson Secondary, it was HO-8 that handled that run as well. As I recall, HO-8 ran Monday thru Friday while I was employed by NJT.
At night there was an HO-9 (I believe that was the symbol) that worked out of C.H. but since he was usually just starting his shift as I was ending mine I'm not sure what they did.
As for the through freights, yes, they did come up the Bergen County Line. In opposition to what most railroads do with their train symbols, NS did it backwards: 43A was the eastbound, 42A was the westbound. They were general freights that replaced the Conrail OIBU/BUOI. The westbound would usually depart Croxton after 8pm for Suffern Yard. At Suffern they would make a drop of cars for the local (H-55/H-56) and pick up whatever was going west. When I was working on 2nd trick I was usually off-duty before they got to Suffern so I'm not sure what they did once past Suffern, but I think it would be safe to assume that they stopped at C.H. for a drop-off/pick-up as well as doing the same at Port Jervis.
I hope this answered some of your questions. Like I stated at the beginning, this information is slightly dated. Anyone who can provide current information on C.H. operations will be most welcome.
Joe P