Given that .ico files can be relatively large on recent OS' with high-DPI displays and multiple resolution images, it is beneficial to save space by removing the separate .ico files and instead reference the icons via the embedded resource in the .exe when necessary.
This is compounded by the fact that the same .ico file will be made into multiple copies when multiple launchers are used, even if they don't have unique icons.

For some applications the .ico file is the largest file outside of the Java runtime. There is no need to have multiple redundant copies of it.

I attempted to work around this by removing .ico files from the app-image after creating it, but this leads to failures when making an .msi file from the app-image. Shortcut elements in the intermediate bundle.wxf file refer to the .ico files, which is not useful since the same icon is in the .exe they are referring to and specifying a separate icon is optional. E.g. in:

        <Shortcut Id="shortcut99d00e1ede14399d8ee8e9d74ba8b6f8" Name="MyLauncher" WorkingDirectory="INSTALLDIR" Advertise="no" IconIndex="0" Target="[#file64e3276016c53c7cb3719ad2f26bd4f3]" Icon="icon897347353"></Shortcut>

IconIndex and Icon attributes are not needed. See https://wixtoolset.org/documentation/manual/v3/howtos/files_and_registry/create_start_menu_shortcut.html