For one, one can't be certain of order (two columns ordered top to bottom, each, or left right, left right and so on?). But also, just scanability of headlines is slowed.
I don't like dumping on earnest Show HNs, but I have such a strong reaction to sites that just think "oh, it just needs a rebrand to a 'modern' UI". Look, lots of unnecessary whitespace! Borders with rounded corners! And all this ends up doing is making the site much less usable (much harder to scan headlines as you point out) for some abstract notion of "prettiness".
Folks should understand that HN's simplicity and information density is a feature, not a big. I've seen lots of sites ruin themselves (cough cough Slashdot cough...) for the sake of some unnecessary redesign.
The domain click target is too big, it's a div spanning the whole width of the card, so it's easy to accidentally open the domain root instead of the link, especially on mobile, which is something I would probably never intend. (On HN the domain link actually serves a purpose — letting you check prior submissions for the domain.) Making the click target an inline-block as wide as the domain text or simply getting rid of the domain link should be better.
Kind of reminds me of this (not identical, but I think similar) problem.
https://www.nngroup.com/articles/zigzag-page-layout/.
For one, one can't be certain of order (two columns ordered top to bottom, each, or left right, left right and so on?). But also, just scanability of headlines is slowed.