Why do some crystal structure files not include bonds?
If you solve an x-ray crystal structure, you simply get a set of atomic positions. No more, no less.

Often, the atomic positions don't include hydrogen atoms, only the "heavy" atoms.

Thus, most CIF (crystallographic interchange format) files, there are no defined bonds. Somewhere along the way, software perceives bonding information because most chemists prefer to have a valence-bond graph of atoms and bonds (and bond orders).

There are many algorithms for determining a bond graph from a set of atomic positions with varying "accuracy." I put the word in quotes because it's sometimes unclear what the goal should be when determining bond orders. For example, is a molecule in a keto or enol tautomer form? In some cases, the $\ce{C-O}$ bond is not clearly a single bond distance or a $\ce{C=O}$ distance. Maybe there's an ensemble average of both forms.

The standard seems to be if the CIF file looks more "ionic" (e.g., a salt like $\ce{NaCl}$) bonds probably will be ignored, but otherwise, bonds are interpreted from interatomic distances.