We resolved the issue by recreating the Synapse Serverless database inlc. recreation of the database MASTER KEY. Since then the issue did not occur again, but the underlying reason is still unclear.
It may be the case that recreating the MASTER KEY is sufficient to get rid of the issue, we just recreated the database using our infrastructure scripts and did not test it independently. As mentioned in the original issue description, recreation of other elements (e.g. scoped credential) was not sufficient.
While debugging we also discovered that the error message sometimes changed to
Error: handling external file: 'Invalid: Parquet magic bytes not found in footer. Either the file is corrupted or this is not a parquet file.'. File/External table name: <path to file>
when running the query in Synapse. It was not possible to make out a deterministic behaviour for when which error message will be displayed.