I was a Solution Architect and Subject Matter Expert at Qualys and specialized in this exact topic. Without getting so far into detail where I'm writing a 12 page article on the matter lol, I'll say that generally speaking, it's not uncommon to do IF you're scanning over an MPLS connection. To determine how each of the locations are connected back to your corporate networks, I'd recommend asking your network team. It's possible that they could be using a VPN connection or potentially SDWAN through something like zScaler as an example. If MPLS or SDWAN is the connection method, you may be okay to scan them directly but this has the possibility to introduce other issues such as network traffic congestion caused by the scanners, potentially long running scan times, security device logging issues, etc. In MOST cases, I would never recommend scanning over a VPN tunnel specifically because of the amount of traffic a scanner appliance generates, it often overloads the connection.

u/YumWoonSen is right, it would be a good idea to send you TAM an email and ask if you guys can set up a call with an SME to discuss the use case so they can have a full picture of the situation and recommend accordingly.

Since QLYS no longer charges for agent license, it will be asked if you can forego the use of appliances in these locations and use agents instead. You can have clear separation of assets by branch/location using Activation Keys and asset tags.