This actually is a legit issue, and doesn't have much to do with CLI itself, deprecated or not.
There is currently no way to access columns that aren't part of column_metadata (the dynamic part of 'mixed' Thrift column families), only the static part.
Except removing all the column_metadata entirely, so that it would become a dynamic column family. You'll probably want to change default_validation_class to BytesType then, too.
Then you'd be able to read all the data via CQL, treated as dense tables.
We'll have to find a way to do this in a better way, eventually, probably, but for now that's the only workaround.