Just a personal opinion, I use a simple rule-of-thumb when it comes to running any variety of Smarten Punctuation.
If the book contains computer code, don't do it -
ever. The idea that one can use one-size-fits-all magic cleanup routines is madness. Best to employ the 'little grey cells' at all times.
It's possible that some Smarten routines may leave alone text inside <pre> tags, but I wouldn't rely on that without extensive testing. The use of <pre> tags isn't very ereader-friendly in any case.