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I already have Origin as part of a humble bundle, but it was never patched and I heard that people had problems with Origin crashing.

I want to know if gog ever released any kind of patch for Origin that would justify repurchasing it on gog.

This question / problem has been solved by Bethezerimage
There is no changelog for the game in the Library, so I would say there was nothing since the game was added here... but then again - maybe there were patches before GOG started selling Ys Origin?

So, in general answer to your question - no this is, most probably, the same version you have from Humble, minus drm (I don't know if they offered it drm-free or steam key only).
Thanks for the info!

The Humble version is DRM-free, yes.