I run some scripts off crontab. They could cause a problem if they run while I
am manually using nmh. Fortunately, they are run at night when I am likely to
be asleep. I run them at night not to avoid clashes but to not use computer
cycles and disk accesses while I am doing manual stuff. BUT on rare occasions
when I have insomnia there could be clashes. From now on I will try to
remember to be careful.
I don't have any such code handy, but it seems like one could put smarts into the cronjob to either sleep or abort if you are active or have been recently (for your definition of that). Basically, look at the output from the "IDLE" column of the "w" or something similar. Since that looks at terminal idleness, and nmh is all CLI based, if you are using a web browser or the like, there won't be a conflict. If you are using mh-e, exmh, or the like, there could be as I am not sure how they show up. There is still a corner case where the cronjob starts and then you start doing something in nmh of course.
Hope this helps.