I have a few questions.
I will be using mssql and windows server.
When configured as in case 1, how much software is used?
Is the OS included in the Database?
Can data be synchronized when data is stored on its own hard disk like case 2?
Ignition doesn't provide the database. You provide the database. A database that supports high availability is recommended when using redundant Ignition gateways. Ignition only understands "Case 1". Putting the database on separate hardware is highly recommended. "Case 2" is entirely a feature of the database product you choose.
Databases and OSes are different things, and if commercial, may need to be paid for separately. These aren't Ignition questions, per se. Since you've chosen Microsoft products, you should be asking Microsoft about MS SQL redundancy and licensing.