For me, the stress in Hypothese is on the third syllable. But I've also never heard Germans put the stress on the first syllable in hypothesis. More often I hear it on the third, following the German pronunciation.

I think that's right. In German I hear it as [Hyp]o[the]se with equal stress on each [.] In contrast to the (typically mad) English spelling sound mapping where it's hy[poth]esis but still [the]sis. imho the real question is why English is so weird, not why do Germans pronounce hypothesis oddly 😆