So here’s where it gets interesting. I was doing some further research and the only place I can find mention of deprecation is in the WebKit API class documentation on the Apple Developer web site. But that’s a program’s internal representation of said archive, not the file format itself. This class is marked as “available” from macOS 10.13 through 10.14, which is the 2017 and 2018 releases and must therefore be deprecated from 2019.
However, further digging unearthed the fact that the 2019 release of iOS & iPadOS 13 introduced a new ability to save and view .webarchive files. You can see information about this in the MacStories iOS and iPadOS 13 review here.
So, I don’t think the .webarchive file format is going away at all, if this functionality was introduced the year after the API class was deprecated.
I’m sticking with .webarchive for now because there are some pages I tried to convert which do not convert well to PDF.