The only justification for the synonym I could find was in the answer to Why is "query" a suggested synonym for "sql"?:
Simply because when the site was young, we repeatedly had folks posting questions about "query" when they really meant "help me with my sql" and don't understand the esoteric differences of the description of higher order math and the relations of sets.
..which seems less than compelling.
The current sql excerpt says:
Structured Query Language (SQL). For questions about the language, not Microsoft SQL Server (tag sql-server).
For query the (hard to locate) excerpt is:
Writing queries to request or change information stored in a database or other information management system. Questions should include table and index definitions, sample data, expected output, and a tag for the specific system (e.g. MySQL, PostgreSQL, Oracle, SQL Server, MongoDB).
That seems different enough that the synonym ought to be broken.
There are other questions around the usefulness/usage of both tags, but those are separate issues that we should discuss, er, separately.
Other (somewhat) related Q & A: