Sorry, meant to address my previous message to Michael. :-)

I've done a little digging, and according to the first-level results from:

apt-rdepends --reverse --show=Depends,Recommends,Suggests ca-certificates

The only MUAs that depend, recommend, or suggest ca-certificates are
mutt and Sylpheed.

Sylpheed uses ca-certificates just for SSL:
https://github.com/jan0sch/sylpheed/blob/master/libsylph/ssl.c#L58.

Mutt seems to be the only MUA that uses ca-certificates for S/MIME. It
ships with /etc/Muttrc.d/smime.rc, which has:

set smime_ca_location=`for f in $HOME/.smime/ca-certificates.crt
$HOME/.smime/ca-bundle.crt /etc/ssl/certs/ca-certificates.crt ; do if [
-e $f ] ; then echo $f ; exit ; fi ; done`

These are the remaining CAs in the latest version of ca-certificates
from git that are present only because they have the email trust bit:

"Verisign Class 1 Public Primary Certification Authority - G3"
"Verisign Class 2 Public Primary Certification Authority - G3"
"UTN USERFirst Email Root CA"
"SwissSign Platinum CA - G2"
"AC Ra\xC3\xADz Certic\xC3\xA1mara S.A."
"TC TrustCenter Class 3 CA II"
"ComSign CA"
"S-TRUST Universal Root CA"
"Symantec Class 1 Public Primary Certification Authority - G6"
"Symantec Class 2 Public Primary Certification Authority - G6"
"Symantec Class 1 Public Primary Certification Authority - G4"
"Symantec Class 2 Public Primary Certification Authority - G4"

It's entirely possible that none of these CAs are actually used for
S/MIME by any Mutt user. For instance, Symantec end-of-lifed their email
offering in August 2016:
https://www.symantec.com/products/information-protection/digital-ids-secure-email.
ComSign doesn't offer email certificates anywhere on their site:
https://www.comsign.co.uk/. VeriSign was bought by Symantec ages ago.

After doing this research, I'd actually argue in favor of dropping these
CA's from ca-certificates outright, without making special provision for
S/MIME.

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