Response from support:
Currently, IFTTT and other integrations like Google Home and Alexa can only be installed on one account. This is a limitation of both SmartThings and also IFTTT/Google Home/Alexa. At the moment, the only way to authorize IFTTT is to set up each Hub on a separate email account for both SmartThings and also IFTTT. While IFTTT may be able to see each location since they are tied into the same email IFFF lacks the logic necessary to differentiate between locations. So if you triggered the applet in IFTTT it would randomly select one of those locations as it is not capable of being able to select a specific location, even though you selected a specific location. This is why you would need to have the separate accounts.
If you wanted to do this you would need to Factory Reset one of your Hubs and set it up in a separate SmartThings account as well as a separate IFTTT account. I apologize for this inconvinence. We would love to be able to offer multiple location access to these services and I have added this as a feature request on out internal page on your behalf.