If you have an account you would like to hide from certain areas of Monarch, there are several options under the "Edit" menu to do so. Each options lets you hide different parts of the account depending on what you are trying to accomplish. You can select to hide the account in the account list, hide the balance from your net worth, and/or hide the transactions relating to the account from your cash flow and budgets.
If the account has been permanently closed, it is best to select the "Close account" option. This will hide the account from your list but preserve all its history. You can also select to "Delete account," which will remove all data completely.
The "Edit" menu is found as a button in the top right of the web app once you have clicked into any account, or in the 3-dot overflow menu in the mobile app.