This is by design. jam install installs everything, and it cannot detect which parts you have manually compiled.
Apart from this, you do need the plugins.. otherwise you won't be able to use the lib for anything really

ok, but though it's usefull to skip building the apps.
Because jam cannot see what I have manually compiled, wouldn't that justify three new targets "appinstall", "libinstall" and "pluginstall"?
jam install makes those three targets then. Just an idea.
(Maybe I have libs and plugins installed yet but want to replace the libs, then jam install would make everything.)
This is how I prepare CS for my project within a shellscript with avoiding the compilation of the apps:
cp mk/jam/install.jam mk/jam/install.BACKUP
sed -e "s#INSTALLTARGETS = install_bin install_plugin install_lib install_include#INSTALLTARGETS = install_plugin install_lib install_include#" mk/jam/install.BACKUP > mk/jam/install.jam
./configure --prefix="$PREFIX" --sysconfdir="$PREFIX"/lib --without-python --without-perl --without-java --without-wx
jam $J cs-config plugins libs masterheaders
jam $J install
cp cs-config "$PREFIX"/bin
jam clean
mv mk/jam/install.BACKUP mk/jam/install.jam
I think that most of the projects don't need the apps, because they are for testing/learning/demonstration purposes only; not for distribution with their projects.
Compiling the libraries as shared libs is work in progress, not tested really and probably broken (this includes the installation of them)
Compiling works for me (though I'm not able to test the shared libs because I use CEL too and that won't compile with CS' shared libs).
This however paritally sounds like a bug. Maybe you could reserach and provide a patch? Otherwise it will probably not be fixed until next release.
During the development most/all of the CS developers don't install but keep CS in the build directory (and set $CRYSTAL when running other things) so jam install breaks every now and then. Before a release it is usualy fixed so that it works for the releases though.
I tried to fix that a half year ago but jamfiles are too cryptic for me: I tried to find out how to use jam at the beginning of my project, but I didn't understand that system/the docs (that's why I use scons in my project), so I cannot help you with jam-issues, sorry.