I would suggest the following
1. Run SQL Profile and run a test, see who the connection comes in as, and the query runs, and the results it says you get, as the Connector itself, by proxy isn't going stop results unless something is configured wrong
2. Verify permissions. If you do step #1 you should easily see if the account running the query has permission to the table and can run etc etc.
3. Wrong instance of SQL Server/Database, just verify for sure you dont have multiple copies and that you are in fact hitting it correctly (which #1 will do as well)
Also, look at the flow run itself, are you certain the output is zero rows and not an issue with the rest of the flow?
Are you using SPNs? User Account? etc.
The biggest is simply #1 should take no more than a few moments then look and see what account/issues it might have had.
That or you are hitting the wrong instn