For the train numbers, they are used in block_id instead of trip_short_name. The calendar_dates.txt is similar to the LIRR because NJT GTFS does not use calendar.txt
As for the bus route numbers... Not only do they have the route number on route_short_name column, but they also have it in the trip_headsign column with each trip's destination.
They don't use the route_id column as an internal reference, but it would be nice if they did.
What they do have, which because their fare system is so complex is they put "-Exact Fare" at the end of the trip_headsign column only on bus routes where the fare payment is exact and the driver has no change.
NJ Transit should do what Metro North does and put stop_URL link to every train station and light rail station because they have a page to each of those stations on their website.