IHO actually mentions two test data sets. One is shown and discussed above, the other (much more comprehensive, but older) can be found at IHO's S-64 page as Unencrypted ENC Test Data Set
(4.5 MB). I think some of the checks there may be relevant.
Specifically, I turned to this test set when examining how updates to S-57 charts
are handled (.001, .002...). This was the only place I could find any test data.