Ok, back from a few days off and on my regular machine. No idea why my comments were getting eaten when posting from my iPad, I tried different browsers, did a Preview before posting, no luck.
Based on the info in several KMS articles, it looks like everything in /etc/cron.daily is run during the NP nightly maintenance, I'm not sure on exactly how, but the /etc/crontab file specifically warns not to edit as it will get overwritten, so Mitel is doing something weird under the hood. To make things simple, just add your commands to the /etc/cron.daily/89NPMdaily file. Grab a copy of the original file first, of course. Open it up in vi or nano (ssh in, go to the /etc/cron.daily and "nano 89NPMdaily" or "vi 89NPMdaily"), add a comment line and then your shell commands, then save the file. Save a copy as well, as I would imagine this will get overwritten on an upgrade.