Unfortunately SQL Developer doesn’t fully honour the set echo off command that would (appear to) solve this in SQL*Plus.
The only workaround I’ve found for this is to save what you’re doing as a script, e.g. test.sql with:
set echo off
spool c:\test.csv
select /*csv*/ username, user_id, created from all_users;
spool off;
And then from SQL Developer, only have a call to that script:
@test.sql
And run that as a script (F5).
Saving as a script file shouldn’t be much of a hardship anyway for anything other than an ad hoc query; and running that with @ instead of opening the script and running it directly is only a bit of a pain.
A bit of searching found the same solution on the SQL Developer forum, and the development team suggest it’s intentional behaviour to mimic what SQL*Plus does; you need to run a script with @ there too in order to hide the query text.