I don't really care about whether the coverage is a percent more or less. But if you want to have the nodoctest.py functionality then the marked directories should not be counted.
Incidentally, about the legacy code for loading old notebooks: here is one lesson to be learned about long-term support of data files. The only sane way to handle this imho is:
* The current code can read/write the current data format
* Whenever you upgrade from format version N to N+1, you write a self-contained updater.
* Old files are sent through the chain of updaters until they are current.
Invariably, any project will start out with the old-version-tolerant loader approach. Its a nice quick solution in the beginning, but as time progresses it'll get more and more difficult to support.