> That paper is about factotum which was introduced in 4th edition, like I said.

Which describes that yes, there was security in Plan 9 prior to Factotum, just that it wasn't good enough.

> Regardless, I'm more talking about the fact that transport encryption still isn't used ubiquitously to my knowledge.

It certainly is. You get SSL/TLS for free on Plan 9 as its a service. You dont mess with security code and instead use tlssrv(8). See https://man.9front.org/8/tlssrv