QM9 dataset with chirality
I don't know about that particular GitHub archive, although I'll point out that the smiles.csv contains several kinds of SMILES - the final column containing the correct SMILES.

IMHO, this is an unfortunate result of people mis-using SMILES. As you note, it's perfectly possible to take a chiral molecular structure and output a SMILES with no stereochemical information.

Take alanine - to a chemist, if you simply say 'alanine,' they immediately think 'amino acid' and translate to L-alanine, or C[C@@H](C(=O)O)N as the so-called "isomeric SMILES":



Unfortunately, if you go to PubChem for L-Alanine, you'll see a "canonical SMILES" which sounds official and is CC(C(=O)O)N - no stereochemistry!

The official version of QM9 can be found on FigShare based on the corresponding publication.

While the official files are in a somewhat non-standard XYZ format, they do have the stereochemically-correct SMILES at the end of the file, e.g. C1N2[C@H]3[C@@H]4[C@@H]5O[C@]13[C@H]2[C@H]45 Just watch that some numbers are formatted like -8.0386*^-6 (i.e., $-8 \times 10^{-6}$) and can sometimes be misinterpreted by programs like Open Babel or RDKit .. practically everything I've seen.