Should I prefer an AMD or Nvidia GPU for studying graphics programming, especially with respect to vendor specific debugging tools and ecosystem?
If you want to learn OpenGL X.Y or DirectX A.B then shop for hardware that supports that specification. 

If you're using other software (Blender, Maya, 3DSMax, etc) you'll want to make sure it's supported.

If your OS has a history of issues with a particular vendor, adjust accordingly.

Beyond that, it's not going to matter much, especially at the hobbyist level.
Price / performance metrics are still relevant, it's just that the definition of performance is different.