why is the markdown geany plugin missing from the repository?

The answer to your question is contained in package changelog:

geany-plugins (1.32+dfsg-3) unstable; urgency=medium

• [67b34ed] Disable webkit-using plugins: markdown, webhelper
  webkitgtk-3.0 is not to be used as it is deprecated, but the port to
  webkit2gtk-4.0 isn't ready yet.

Then the Markdown plugin was re-enabled starting with version 1.37+dfsg-5 which came with 21.04.

So currently there are two Ubuntu versions with geany-plugin-markdown package - 21.04 and 21.10.

If you need to compile geany-markdown-plugin on 18.04 LTS use the patching and compiling method below:

software-properties-gtk # enable Source Code here, reload the lists

# get
sudo apt-get build-dep geany-plugins
sudo apt-get install libwebkitgtk-3.0-dev fakeroot

cd ~/Downloads
apt-get source geany-plugins
cd geany-plugins-1.32+dfsg

# patch
sed -i "s/--disable-peg-markdown/--enable-peg-markdown/" debian/rules
sed -i "s/--disable-markdown/--enable-markdown/" debian/rules

cat <<\EOF > ~/Downloads/debian-control.patch
55c55
< #        geany-plugin-markdown (>= ${source:Version}),
---
>          geany-plugin-markdown (>= ${source:Version}),
469,478c469,478
< # Package: geany-plugin-markdown
< # Enhances: geany
< # Architecture: any
< # Depends: ${geany:ABI}, geany-plugins-common (= ${binary:Version}),
< #         ${shlibs:Depends}, ${misc:Depends}
< # Description: markdown plugin for Geany
< #  This plugin provides a real-time preview of rendered Markdown in Geany.
< #  .
< #  Geany is a small and lightweight integrated development environment using the
< #  Gtk+ toolkit.
---
> Package: geany-plugin-markdown
> Enhances: geany
> Architecture: any
> Depends: ${geany:ABI}, geany-plugins-common (= ${binary:Version}),
>          ${shlibs:Depends}, ${misc:Depends}
> Description: markdown plugin for Geany
>   This plugin provides a real-time preview of rendered Markdown in Geany.
>   .
>   Geany is a small and lightweight integrated development environment using the
>   Gtk+ toolkit.
EOF
patch debian/control < ~/Downloads/debian-control.patch

# compile, build and install
cd ~/Downloads && apt-get source -b geany-plugins
sudo apt-get install ./geany-plugin-markdown_1.32+dfsg-3_amd64.deb

Then launch Geany and enable the plugin from in it using Tools → Plugin Manager and enjoy.

For Ubuntu 20.04 LTS this method may be adapted as follows:

software-properties-gtk # enable Source Code here, reload the lists

# get
sudo apt-get build-dep geany-plugins
sudo apt-get install libwebkit2gtk-4.0-dev fakeroot

cd ~/Downloads
apt-get source geany-plugins
cd geany-plugins-1.36+dfsg

# patch
sed -i "s/--disable-peg-markdown/--enable-peg-markdown/" debian/rules
sed -i "s/--disable-markdown/--enable-markdown/" debian/rules

cat <<\EOF > ~/Downloads/debian-control.patch
55c55
< #        geany-plugin-markdown (>= ${source:Version}),
---
>          geany-plugin-markdown (>= ${source:Version}),
469,478c469,478
< # Package: geany-plugin-markdown
< # Enhances: geany
< # Architecture: any
< # Depends: ${geany:ABI}, geany-plugins-common (= ${binary:Version}),
< #         ${shlibs:Depends}, ${misc:Depends}
< # Description: markdown plugin for Geany
< #  This plugin provides a real-time preview of rendered Markdown in Geany.
< #  .
< #  Geany is a small and lightweight integrated development environment using the
< #  Gtk+ toolkit.
---
> Package: geany-plugin-markdown
> Enhances: geany
> Architecture: any
> Depends: ${geany:ABI}, geany-plugins-common (= ${binary:Version}),
>          ${shlibs:Depends}, ${misc:Depends}
> Description: markdown plugin for Geany
>   This plugin provides a real-time preview of rendered Markdown in Geany.
>   .
>   Geany is a small and lightweight integrated development environment using the
>   Gtk+ toolkit.
EOF
patch debian/control < ~/Downloads/debian-control.patch

# compile, build and install
cd ~/Downloads && apt-get source -b geany-plugins
sudo apt-get install ./geany-plugin-markdown_1.36+dfsg-1_amd64.deb