It is a bit more nuanced than that. An incorrect unstated assumption here is that schizophrenia or depression is a singular disease rather than a group of observable symptoms where any two cases may or may not have the same underlying cause.

There are certain types of schizophrenia that are highly heritable and others that are more sporadic. Highly pathogenic variants tend to be very rare because those regions of the genome are under evolutionary constraint.

GWAS are used is to figure out which genes may be involved in the pathology. So we are essentially looking at rare cases of inherited disease to figure out which genes might play a role in more common non inherited versions.