I suppose you're right but can anyone tell the difference once it's on the screen?
Even the initial virtual image is only 2D until it's viewed through 3D specs. We only call it 3D (in the CGI sense) because it can be rotated up, down and around.
I wonder if it's cheaper to convert than to render everything twice to get 2 viewpoints?
If we're talking pure CG animated films, here's how it breaks down:
All DreamWorks animated titles including Monsters vs. Aliens and after are "real" 3D
All Pixar titles released thus far are also "real" 3D. Anything that has been rendered in 3D for rerelease (theatrical or otherwise) was not post converted, as it was a matter of going into the original files and inserting a second virtual camera to create stereoscopy.
The first 3 Shrek films are post-converted, as DWA lost the original digital files.
Hoodwinked 2: Hood vs. Evil is post-converted.
All BlueSky titles released thus far in 3D are "true" 3D.
All Illumination Entertainment titles except Hop (which was only released in 2D) are "true" 3D.
All nWave Pictures titles are "true" 3D, and exhibit some of the best depth and "in yo' face" moments out there.
Others have to be looked at on a case by case basis.
As for Smurfs, I recall hearing in the press materials for Pirates of the Caribbean: On Stranger Tides that it's apparently less expensive to render the CG in 2D and then convert it to 3D. POTC:OST was shot natively in 3D though, so YMMV.