(If they get there first, this has a side benefit of preventing Windows, Linux and Chrome OS from doing the same thing as easily.)
But seriously: app store revenue is a rounding error. It's more likely that Apple perceives web apps as a threat to their bottom line the same way they view ripped MP3s as a threat to their iTunes revenue.
“Apple’s apps economy: Bigger than Hollywood”
https://fortune.com/2015/01/22/apples-apps-economy-bigger-th...
$14b (app store napkin estimate), out of $265b (2018), is ~5%.
So, your "rounding error" is in reality 17.5% of Apple's entire revenue. It's "only" twice bigger than the entire Mac portion of Apple's business which is $25 billion [3]
[1] https://www.cultofmac.com/601492/app-store-google-play-reven...
[2] https://www.statista.com/statistics/265125/total-net-sales-o...