Is there a way to configure the extra buttons on the mouse, like the side buttons, for SS2? SS2 doesn't recognize the buttons at all; nothing happens when I press them. I also have DPI buttons on my mouse that I'd like to use. These are recognized as mouse wheel up/down when I try to assign them.

System Shock 2 doesn't recognise additional mouse buttons directly. Use your mouse's configuration software to set those buttons to standard keyboard keys, either for this game or overall (if you don't need their original functions). You'll then be able to bind those buttons as keys and they'll work as expected.