net-tools is the old networking tools package that is in the process of being deprecated by sys-apps/iproute2. We still need, and require these tools to set hostname. see the iproute2 page for a list of commands, and their replacements.
hostname- show or set the system's host name
dnsdomainname- show the system's DNS domain name
domainname- show or set the system's NIS/YP domain name
nisdomainname- show or set system's NIS/YP domain name
ypdomainname- show or set the system's NIS/YP domain name
/etc/conf.d/hostname controls the system hostname.
/etc/conf.d/net is where your domain name is defined.
/etc/hosts is where static routes and loopbacks are defined.