They aren't "afraid", it's a simple logic problem. You have 3 platforms at the terminus. You can only have 3 trains in the station. Max. That's basic physics. You can't overlap trains. Anything else has to wait in the tunnel for a slot to open up.

While a train is waiting they also block some capacity for trains to leave the station. It also means if there's a problem on that train (medical emergency, terrorism, fire etc.) there's no easy solution other than wait for a train to depart, or go through the procedure to reverse if there's no train behind it.

From a safety/security perspective, that's absolutely out of the question. Even pre-9/11 that would be wildly careless operating procedures. Trains intentionally don't leave stations in underground transit if they know there's an obstruction ahead that prevents it from reaching the next safe haven.

There's no way people will be understanding if there's a shooting or smoke conditions and the train waited several minutes because "train traffic ahead".

Adding platforms isn't easy on 6th avenue due to subway easements (remember 33rd street isn't actually on 33rd since they already moved that station once for the subway expansion), and adjacent buildings basements being on either side.

The only practical solution would be to build a new station below the existing one, but drilling below an operating station is an insane logistical nightmare as the East Side Access project has shown. NYC is build on heavy bedrock that's not easy to drill, and doing so without disturbing things above it is extremely slow and expensive. It would help if they could just shut down the line for a decade, and/or demo some buildings in the area, but nobody is going to go for that.