Hi and welcome to NethServer Community,
NethServer uses templates to write config files. You could create a custom template fragment to add the line to dnsmasq.conf:
Create custom template dir:
mkdir -p /etc/e-smith/templates-custom/etc/dnsmasq.conf
Create fragment:
echo "conf-dir=/etc/dnsmasq.d" > /etc/e-smith/templates-custom/etc/dnsmasq.conf/91dnsmasqd
Apply config:
signal-event nethserver-dnsmasq-update