OK - I am starting to understand. Apparently client had Firebird default instance Windows registry entry from the Firebird installations of the previous versions. That is why Firebird 3.0 installation wizard did not displayed extended configuration form with the possibility to initialize security3 database and create SYSDBA account. So - it might be possible that I should execute steps from the Firebird 3.0 release notes "Initializing the Security Database".

However, something is still broken. My initialization session ended with error:
C:\Program Files\Firebird\Firebird_3_0>isql -user sysdba employee
Database: employee, User: SYSDBA
SQL> create user SYSDBA password 'masterkey';
Statement failed, SQLSTATE = 23000
add record error
-violation of PRIMARY or UNIQUE KEY constraint "INTEG_2" on table "PLG$USERS"
-Problematic key value is ("PLG$USER_NAME" = 'SYSDBA')
SQL>

So - it reports that SYSDBA account is present!