I wonder if there are options to use an AQL-Query over several Databases?
Using pyArango I know you could write a script that iterates over all databases and executes the AQL, but natively, is that possible?
No, this is not possible. By design, each database is isolated from the others. The documentation states the following:
Please note that commands, actions, scripts or AQL queries should never access multiple databases, even if they exist. The only intended and supported way in ArangoDB is to use one database at a time for a command, an action, a script or a query. Operations started in one database must not switch the database later and continue operating in another.