Subways add cost and complexity, things Stern typically looks to avoid. Typically the VUKs for subways are more complex since they need to have the subway feed it, and often have to support and track more then one ball in those spots (basically a trough, with all of the challenges and reliability issues). It is pretty rare in any game to have balls just fly out of somewhere without some notification to the user about it before it happens (typically via flasher and sound) and certainly in STTNG, the balls are typically fed right to the flipper (or the cannon), so not like it can surprise you and on the flip side there are plenty of scoops that can catch you off guard and the ball comes out where it went in. It reality on STTNG, despite two diverters on the subway, there is just the one exit 95% of the time, since the other two feed the canons, and those are only active at very specific times.
As someone pointed out, it does seem that subways are often used when the ball is captured in a toy and then routed somewhere else to complete the illusion, vs a basic bang toy, and we just don't see those types of toys as often in the newer Stern games.
For games to do well for operators, they need to be reliable and I'm guessing that is another reason (in addition to cost, engineering effort) we see more basic toys and no subways from Stern.
TBL had an issue at its first expo, with balls getting stuck in the subway, but they worked through that. You would not have been able to do the Rug without one, which is a great example of a bang toy that also captures the ball.