I only run 3 additional plugins, and since these are not maintained on GIT, I do my upgrades manually. It is really not a big problem (once you have done it more than 100 times). I do the complete upgrade (including first an experimental duplicate upgrade) in about 20 minutes. My moodle is "down" for about 3 minutes.
Best practices?
1) Prep and experiment.
2) Go into maintenance mode.
3) Backup
4) Install
(I kind of skip step 3 since I have a cron job doing my complete backup each night. Yep, could be a few changes between my regular backup and my upgrade. The data is there, it is just if something crashes that I might lose a little data. If I thought this might be an issue, I would do all four steps.)