I didn't follow the history of those changes, but I looked into the current version of Debian 11 ("Bullseye"). neomutt 20201127.
pgpewrap has been installed to /usr/libexec/neomutt/pgpewrap grep pgpewrap /etc/neomuttrc.d/* shows commands which are using /usr/libexec/neomutt/pgpewrap -- Stefan