The situation is summarised here, and the current status is:

Webhelper, nobody has tested the Webhelper PR #1295 which includes the switch to Webkit 4.1, so I guess it has no users who care, so it should not configure on Debian (and other distros) and not get built when old Webkit is removed
Markdown, nobody has provided a copy of the build patch (no code changes) from #1295, so again it should not configure on Debian (and other distros) and not get built when old Webkit is removed
Updatechecker, really only useful on Windows (or Macos????) where the Geany project provides the binaries, so Debian should be disabling it as it doesn't look at their repositories (porting to libsoup3 will depend on its availability on those platforms)
Geniuspaste, has had no actual functionality changes for seven years, maybe its because it "just works" (oh look, a flying pig ;-) or because it has no users, anyway "somebody" needs to contribute a PR porting to Libsoup3, and until then it should not configure on Debian (and other distros) and not get built when old Libsoup2 is removed

As Geany-plugins is a collection, each plugin individually enables or disables based on availability of its dependencies during configure, so Debian should not have to do anything to have those plugins not build as above.

It should be noted that those on LTS distros (like me) do not have Libsoup3 available, and therefore not Webkit 4.1, so we can't test #1295 or provide any other PRs, but I really doubt that all geany contributors are on LTS distros, so until "somebody" contributes the patches those plugins will not get distributed, and maybe that will trigger contributions.

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