"What tells it that it is a "scan" service? That bit of the puzzle seems to be missing..."

Whatever is the parameter after the @ and before the dot  becomes %i in the service file.  Look at the service file:
[Unit]
Description = clamd scanner (%i) daemon
After = syslog.target nss-lookup.target network.target

[Service]
Type = simple
ExecStart = /usr/sbin/clamd -c /etc/clamd.d/%i.conf --nofork=yes
Restart = on-failure
PrivateTmp = true

so clamd@scan.service invokes clamd with the scan.conf file as it's configuration file.
This way you can have multiple clamd services each using a different config file.  Just create another config file in /etc/clamd.d/my_config.conf and:
ln -s /lib/systemd/system/clamd@.service /etc/systemd/system/clamd@my_config.service

You should have the /etc/clamd.d/scan.conf I think:

[root@moses shorewall]# rpm -qf /etc/clamd.d/scan.conf
clamav-scanner-0.97.5-1700.fc17.noarch

Bill