It appears nothing is ever deleted from the diagnostic.data directory.

This can be reproduced in a few hours by running with --setParameter diagnosticDataCollectionPeriodMillis=100 --setParameter diagnosticDataCollectionFileSizeMb=1 --setParameter diagnosticDataCollectionDirectorySizeMb=10, and putting some load on the mongod (because data rate is very low for an idle mongod where most of the counters don't change).