Yeah, once you have the nag on Emunand, you're screwed. Unless you restore a previous backup or wipe.
If your wipe or restore your emunand, you'll lose Devmenu. If you don't have a Gateway, you'll have to go through the process again.
When you reformat your Emunand, it'll create a new Friend code (same as the one on Sysnand now) & You'll lose everything you've installed.
If you have a Gateway, you can use the EmunandTool to inject your Sysnands NAND.BIN IF you've only had to format your Emunand one time.
You can backup the saves using SaveDataFiler, whatever you've aquired in those saves via streetpass should persist.
In all honesty, it's far more of a hassle than it's worth imo.
I just live with the update nag (I forgot I had the wifi on one day... After getting rid of it before).
I figure why go through the hassle if it's more than likely just going to happen again in the future.
Hang on, I actually found that I did create an emunand backup a few weeks ago. So you're saying if I restore the emunand file I have, it'll remove devmenu? Does it remove all my other installed apps/games too? When you say I have to go through the whole process again, you mean literally the entire process? Man, now I'm thinking it's not worth the trouble. I know you already said that, and I agreed with you before, but that was before I realized I did have an emunand backup.
As for the gateway stuff, I don't think I can restore my nand.bin becuase I think I formatted my emunand twice. The first time was when I was doing this, and then I realized I unlinked my nands prematurely, so I reformatted the emunand again to begin fresh.
Anyways, I guess it's good to know I do have a backup laying around.