The tick box Include only relates to the VAT Return and whether you want to include the VAT code in the VAT return.
If you do not use a specific code and you do not want it to show in the drop-down list for selection you will need to edit the VAT code and mark it as unused in the DPSSQLConfig:
Note: You will need supervisor rights to log in to DPS Config
Click Accounts.
Click VAT Codes.
Click on the VAT code you do not want to display.
Change the description to Unused.
Click Update VAT Code.