First install the stunnel4 package:

sudo apt-get install stunnel4

Provide a stunnel config file:

cat << EOF | sudo tee /etc/stunnel/irc-freenode.conf
pid = /var/run/stunnel4/irc-freenode.pid
setuid = stunnel4
setgid = stunnel4
CAfile = /etc/ssl/certs/ca-certificates.crt
verify = 2

[irc]
client = yes
accept = 127.0.0.1:6667
connect = irc.freenode.net:6697
EOF

Restart the stunnel4 service:

sudo service stunnel4 restart

Now you need to tell Smuxi to connect to host 127.0.0.1 port 6667 in the settings of the IRC server. (Server -> Manage -> select an IRC server -> Edit)

Connect to the updated IRC server. After the connection was established you can check if you are connected using SSL/TLS by doing a /whois your own nick, e.g.:

/whois meebey

This will show the following output:

-!- meebey [~smuxi@123.123.123.123]
-!-  realname: Mirco Bauer
-!-  server: karatkievich.freenode.net [Montreal, CA, NA]
[671 (?) meebey] is using a secure connection
[378 (?) meebey] is connecting from *@123.123.123.123
-!-  idle: 6 [signon: 1/9/2017 4:08:03 PM]
-!-  End of /WHOIS list.

The "[671 meebey3] is using a secure connection" line is the interesting one. It means we are connected using SSL/TLS.