Not all of these issues have disappeared, either. Anyone remember this headline from a couple years ago? The bottom 1MiB of memory space on x86 is just a minefield. It's impossible (like literally impossible) in general to know if certain parts of the address space are actual memory or are some weird part of your motherboard chipset or some other hardware. Windows I think still goes through the "wankery" of depending on chipset drivers to (accurately) know which parts of memory are actual memory.
Thankfully the 16-bit (though actually 20-bit but actually kind of more sometimes kind of but not totally) pains have all gone away. The move to flat 32-bit address spaces was a godsend.
PGP itself is a bit of mess.
For one thing, there's really only one major/popular implementation of it these days, which is GPG. The codebase is arcane. Pretty major security vulnerabilities pop up constantly. It doesn't have stable funding. Several years ago the entire project almost collapsed when the world discovered it had been maintained for several years by a single person who didn't have any time or money to maintain it. The situation is a little bit better now, but not much.
(For this reason, people are starting to use age instead of gpg, as the code is much smaller, cleaner, forces safe defaults, and doesn't seem to have security problems)
But the bigger problem that was never properly solved with PGP is key distribution. How do you get somebody's key in the first place? Some people put their keys on their own personal (https) webpage, which is fine, but that's not a solution for everyone, and doesn't scale very well. Okay, so you might use a key server, but that has privacy implications (your identity is essentially public to the world) and centralizes everything down to a handful of small "trusted" key servers (since there would be no way to trust key servers in a decentralized way). We should probably just have email servers themselves serve keys somehow, but nobody's put that into the email standard protocols.
The fact that keys expire amplifies all the problems with key distribution, and encourages people to do really unsafe things with keys, like just blindly trust them. You can sign other people's keys for them, but that also does not scale very well.
The key distribution problem is something that things like Signal have "solved" with things like phone number verification, but there's really no clear way to solve it on something totally distributed like email.