This happens because the default control account for suppliers, Accounts payable, is hard-coded in the program. When you delete the custom control account, the supplier’s subaccount automatically reverts to that default, so the deletion is allowed. The only time deletion of accounts or groups is not allowed is when there would be nowhere to transfer the transactions already posted there.
The purpose of preventing deletion is to avoid loss of data. In this case, no data is lost. It simply appears under a different control account, the default control account.