Short answer: psilocybin might reduce chronic cluster headache attacks, and the improvement appears to track with changes in hypothalamic connectivity, but this does not prove the hypothalamus is the causal route.
In a small open-label study of 10 people with chronic cluster headache, participants received three oral doses of psilocybin over three weeks. On average, attack frequency fell by about 31 percent, and one person had a prolonged remission; fMRI showed that larger changes in hypothalamic-diencephalic connectivity were associated with larger reductions in attacks. You can read the study summary on PubMed.
However, the trial had no placebo group and a very small sample, so expectancy effects and natural fluctuations cannot be ruled out. The results show an association, not a verified mechanism or definitive efficacy.
Bottom line: promising early signal, but more rigorous, controlled studies are needed to confirm whether psilocybin reduces attacks via hypothalamic pathways.