@GreenHawk84 I'd definitely back things up every now and then (I do it more or less once a month, but it's more because of my lack of availability than anything else), and keep at least two historical backups (in case you backup something that's already broken, you can always revert to a previous safe backup).
I don't update packages nor emulators unless I need to - if it's working and there's nothing new that I really need there, then I don't risk breaking things. The latest thing I've wanted to update for (but still didn't) was several months back when RetroArch launched the lookahead features to reduce input lag. That's one of the key things I'd be looking for. Still, then you read that the latest RA and lr-fbalpha can cause slight frame drops on CPS3 games in certain setups and you struggle to revert those changes if needed.
So, my preference: unless there's a meaningful new feature for you or a critical security patch, I'd stay with what you have that's working for you.
Also, I am a big supporter of keeping the ROMs in a USB drive and the OS in the SD Card. Easier to backup, transfer roms, and also to set up fresh in a worst case scenario.