It's been a long time since I've paid attention to that world, but AFAIK, PEPs are still used and essential equipment for internet-style communication (i.e. TCP over IP) via GEO satellites.

It looks like in this 2022 blog post evaluating latency and throughput over Starlink, they concluded that PEPs were not being used in the Starlink network (and probably unnecessary) due to the lower latency characteristics from use of LEO satellites. They also mention that PEPs are (still) commonly employed by GEO-satcom based operators.

https://blog.apnic.net/2022/11/28/fact-checking-starlinks-pe...