Application Pool Isolation: If the same account is used in the application pool for one of your web applications and central administration, this means that your farm configuration (config DB) is editable by all users and trusted code that is registered in sites in the web application. If you can trust your developers, this is not going to be a problem, otherwise this can lead to malicious code injection and loss of your config DB in a worst case scenario.
Highly Available Central Administration Capability: If you have Only one instance of the SharePoint 3.0 Central Administration in your farm installation, you better make sure that you can administer the farm in case of a failure of a server hosting SharePoint 3.0 Central Administration. Best practices recommend that you should have SharePoint 3.0 Central Administration installed on at least two servers in your farm.