Hello Laurens van de Venn,
Welcome to the Microsoft Q&A Platform! Thank you for asking your question here.
Based on the information shared, I understand that you have an external system accessible via REST API, and you want to call these APIs through a Logic App.
If this understanding is correct, you can leverage the HTTP action/trigger with the respective authentication methods in headers to call the external system.
https://learn.microsoft.com/en-us/azure/connectors/connectors-native-http?tabs=standard
Regarding whether these API calls should go through APIM, could you please provide more details on the exact location of the APIM? Is the APIM situated between the Logic App and the external system, and are they communicated via public internet, or are there any traffic restrictions?
Also, if possible, could you please share the high-level architecture diagram and request flow to better understand the issue?