I don’t see the suggested workaround from the DataTables documentation you linked among the things you tried. The docs say:
If you are willing to accept the error (for example if you cannot alter the backend system to fix the error), but don't want your end users to see the alert() message, you can change DataTables' error reporting mechanism to throw a Javascript error to the browser's console, rather than alerting it. This can be done using:
somehow not trigger datatable javascript properly. I dont have deep knowledge about datatable and shiny, dont know what to do now. I ever tried to traced to the original datatable.js file and tried to remove the "alert" line of code but dont know how to merge back to shiny sadly.....