Niels Beukenkamp Thanks for posting your question in Microsoft Q&A. Quota By Counter Keys - List By Service API return quota-by-key for a specific APIM instance (All APIs under the APIM). Based on your description, I assume you are looking for an API to return the values for multiple APIM instances under a subscription/resource group at once.
Unfortunately, it is not possible right now and you would need to make a call for each APIM instance in a subscription and loop through all instances via PowerShell, CLI or SDK scripts (sample reference) of your choice. If you are interested this feature request and like to submit it to our product team, please do so via https://aka.ms/apimwish and others with similar interests can upvote your idea too.
Let me know if you have any additional questions.