The Shell will try to read Zookeeper values from accumulo-site.xml whether it has to or not. Using the Zookeeper CLI options (-z or -zi and zh), the user provides enough information that the shell doesn't need to read the values from accumulo-site.xml. This can be reproduced easily by starting accumulo and then running these commands (from accumulo home):
chmod 000 ./conf/accumulo-site.xml
./bin/accumulo shell -u root -z instance17 localhost:2181
This will produce a FileNotFoundException (Permission denied), with different stacktrace depending on the version.