The short version is that if your application is still using the webkit2gtk-4.0 pkg-config module, then it is using a version of WebKitGTK that uses libsoup 2. The first stable version of WebKitGTK to include support to use only libsoup 3 will be 2.52.0, to be released in March 2026.
Those applications that need migrating and are not yet ready can switch to webkit2gtk-4.1 and still keep using GTK 3.
More details and migration tips in the following piece of news: