Yes, if you put Snort or Suricata on the WAN interface of your main office, then the package would see all traffic. However, if you use NAT, the usefulness of the IDS is diminished a bit in that the only IP addresses you would ever see in the alerts will be those for the far-end Internet host and the WAN IP of your main office firewall. It would be difficult in that scenario to track which host on your private LANs might be infected with or the target of malware.
If you instead run the IDS on the LAN interfaces, you would see the IP addresses before they were NAT-mangled. With the site-to-site VPN scenario you linked, I don't if the LAN approach would work.
Bill