No, the problem is your graphics card unless you are really missing the graphics plugin dll in your Plugin folder.
Project64's error message (D3DERR_...) means that, as soon as the program starts, the emulators queries your video card whether it'll support the graphic plugin currently in use. If the query fails, the graphics plugin cannot be used because the video card seemingly failed to return necessary info about Direct3D support. (failed to initialize).
The part "missing or invalid" means that the emulator always expects the graphics card and its drivers to be faultless, regardless of what the result of the aforementioned query was. It [should] also alert the user into checking that there really are plugins in the Plugin folder and the files within are really the files Project64 can use.
If you've download the official Project64 package, there are no missing plugins, and none of the plugins are invalid/broken.