On the SmartCollection reference it states next to the manual sort_order property that "Deprecation will begin in 2020".
However there's a section for "Update manually-sorted products in the smart collection" which shows how to achieve just that, and it says nothing about deprecation.
So, will it be possible to manually sort products in Smart Collections?
I was pointed to this thread by a Shopify guru when I asked them about the deprecation note. As far as I understand they are not ready to discuss publicly what's going to happen. This leaves me befuddled why the note is in the docs in the first place.
However, I've managed to dig up this thread from 2018 talking about changes to the API in this regard which, as it seems, have not yet been implemented - https://community.shopify.com/c/API-Announcements/Upcoming-changes-to-SmartCollection-API/td-p/44588...
Beginning in mid October, it will be possible to sort some products manually within smart collections. This lets you set a smart collection to any automatic sort order, and then specify a subset of products to be sorted manually. Any products that aren't manually sorted will be automatically sorted according to a specified automatic sort order.
This change means that the manual setting of the sort_order property will be deprecated, and that the order endpoint, like Shopify's admin, will be limited to manually sorting 250 products.
This leads me to believe that by removing the "manual" option from "sort_order" would not remove the possibility of sorting products (somewhat) manually. That's probably why there's still a section about that in the docs.