GWAS studies are extremely expensive studies, often in the hundreds of thousands of dollars in SNP chips alone, and will get published somewhere, somehow. If they don't find results they get published in lesser journals, because there's always something to be said even if there are not significant associations.

It's the same with academic clinical trials, even negative results get published, because for those academics they still need something to show, and a publication of a negative result is better than nothing.

Non-publication bias is more common in less expensive, more exploratory settings, where there are lots of little experiments going on all the time. This is quite different from GWAS.