IIRC former jailbreaks used to have a built in tweak that blocked the update badge and notification. If not the jailbreak itself, Cydia automatically installed a tweak that did as much. I'm not up to date with the jailbreak scene so I'm not if there's currently a stand alone tweak for that. You might check and see if No Update has been updated.
I had a similar issue with this when I had to restore and re-jailbreak the other day. Well, sort of. I didn't get the popup like that, but my settings app still had a "1" in General, meaning software update available. I didn't want that to stay there, so I removed it by removing a specific coding in iFile. Of course, your situation I am assuming is totally different possibly.