I've been using the cargo-update subcommand to update installed binaries for a long time, today after checking for updates with cargo-update I noticed that the only package checked for updates was topgrade, but over the years I've installed many others binaries with cargo, indeed my .cargo/bin folder contains many others packages, but cargo install --list only shows one package, is there any reason why this could be happening or it could be a bug to report?
Do you have an old version of cargo-update? Cargo has switched from git registries to sparse index, and old tooling may be looking at the git checkout that doesn't get updated any more.
cargo keeps information about installed crates in ~/.cargo/.crates.toml and ~/.cargo/.crates2.json.
So if cargo install --list isn't telling you anything anymore, then most likely these files have been modified. You should try figure out what touches them.