The security device is optional at account setup (at least for me it was and I declined it). It recommends it during the account setup buy you can decline it at that time. However, once the account is set up you cannot remove it. Also certain forms of withdrawal and transfer of funds require it to be used (otherwise you have to use a reduced set of options to transfer funds).
I believe you can opt out of security device even after you started using it. Just contact IB support and explain that you are an API client. You may have to sign and fax some forms. A safer way is to set up a second login linked to the trading account and opt out of the security device for this new login. This way you can permnission the new login for trading but withdrawals from the account will still require the original account login and use of a security device.