Tbf if you have an older Sound card for instance it's a relief that you don't have to spend money on the same card but with a PCI-E connection just to be able to keep using a card that you were already satisfied with.
Asus and MSI still have them on a lot of Z170 boards too. Out of 73 Z170 motherboards on
this page, 23 still have a PCI slot, so it's not like every motherboard you buy has a couple of them, but if you need one, they are available.
Besides, there are plenty of features on motherboards that I don't use? I don't see why having these slots on there and not using them is such a problem when the slot layout still allows for a dual GPU + PCI-E 1x slot setup.
They're black anyway, so it's not like they're a massive eyesore and adding more PCI-E 16x/1x lanes would do anything either considering the maximum amount of lanes available from the CPU on this platform.