My understanding is that even if it had passed with flying colours, Obama would have vetoed it. So all of this process is just for show.

Your understanding is incorrect. This was an amendment to the NDAA. Basically the bill that Congress has to pass every year to authorize the government to maintain a standing army, and fund said army. Without the NDAA, our military would effectively cease to exist.

It would be impossible for President Obama to veto it.

Oh so weird riders for special interest causes are okay now?

They always have been in the past.

I wouldn't call this a weird rider. The NSA is a DoD agency, and the NDAA is one of the tools that Congress uses to regulate the DoD.

If it had passed with flying colors, pressure on the Obama to not veto it would be tremendous.

Well, I want it to get to that. I want it to be on Obama's desk and see what happens.

I prefer that to just sitting around.

He's already been reelected, so he doesn't care what the general public thinks of him.

True that he doesn't care per se, but as I doubt he's going to quietly retire to a Hawaiian villa in 3.5 years, he does have to gauge who thinks what of this presumably unexpected issue & backlash.