Also, it might not validate interdependencies between the file you're editing and the other files in your project/application. You can see an example of this if you open a Java file for editing in TextPad, type in a deliberate syntax error, and then save the file. The error will not show up immediately in the WebSphere workbench like it would if you were using the default editor, but rather will appear when the file is rebuilt/recompiled through other means.
Another problem you can run into when using an external editor like TextPad is accidentally opening multiple copies of the same file. Each time you double-click on the file a new TextPad instance will open containing the file's contents. This is in contrast to the way that the default WebSphere editors work, where double-clicking on the file again will either open the file or open the already existing window containing the file.
So, the choice is yours, use WebSphere's default editors or any editor you choose. WebSphere Studio's powerful customization abilities allow you to truly work the way that you want to work. But be sure to use your power wisely, and make sure your choice makes you more productive rather than less productive.