Not the person you're replying to and I don't work for the MTA but some of the radio boxes you are seeing are likely Ultra Wideband radio beacons used for train positioning.

Similar concept to GPS but instead of satellites (which aren't so good when the trains go underground or even when they are above ground but have high building skyline obstructions) the train positions itself based on time-of-flight pings to these beacons with known locations and using multilateration to figure out where the train must be based on the distance information.

Source: Working for a company in San Diego (but travelling to NYC often) I wrote a now surely obsolete version of the positioning code (running in MISRA C on what were basically Raspberry Pi devices installed on the trains) back during the proof of concept phases of this system when it was only the 7 line 5-ish years ago back when Andy Byford was still running things.

Spent a lot of late nights on 7 line trains doing real world tests (exciting when we tested the failsafes and the train had to e-brake!) and had to get trained up to be able to walk the rail lines as we'd often be installing the track-side beacons ourselves during low traffic transit times (which is to say, usually in the middle of the night).

If you watch the video here:

https://www.railwayage.com/news/positioning-the-next-generat...

and go to 1:32 you can very briefly see another thing I wrote there, an app which would take the positioning information in real time and overlay it on to openstreetmaps data.

That app was written in Qt/C++ and wasn't even really part of the system, it was just something I wrote to make it easier to debug any problems with positioning when we could visualize them in a real world context. Generally the only time you'd have positioning errors to debug were due to some of the beacons having incorrect coordinates (I'm sure they've ironed this out a lot since the PoC). The debug app ended up being nice and flashy for the media attending the PoC demos though (more exciting to look at than some text logs) which was a nice side benefit.

This is typical of old buildings that get new technology. Almost never will the old wiring / conduit be demoed when something old gets removed. Just left in place, then who ever installs the new stuff comes along and gets to add even more conduit and wire. Even to just add stuff to an existing location, you would think oh there's already conduit from A to B no problem, Probably still going to end up with new conduit ran. This kind of stuff can be anything from abandoned old analog phone lines to CCTV to even old AC power stuff occasionally.