That happened because they introduced a new weakness to Morlun: vulnerability while feeding. He should still be extremely durable otherwise.
Morlun always was a bit too powerful for a Spidey villain so I'm not surprised they gave him more weaknesses. After all, weakness-exploitation is the only way Spidey can defeat him (he was given a radiation weakness in an earlier storyline for this purpose).
That's not canon it's from Spider-Man a Life story where he ages in real time.
This is how vulnerable Morlun is while feeding in 616
https://comicnewbies.files.wordpress.com/2018/10/death-of-spider-man-noir-1.jpg
https://comicnewbies.files.wordpress.com/2018/10/death-of-spider-man-noir-2.jpg
The irony is since Morlun is multiversal every showing in What If...'s and what not should actually be him, while it obviously isn't the case here.