Strange.
When you disable Settings > Preferences > MISC > ☐ Enable Notepad++ Auto-updater, then exit and reload Notepad++, is it still disabled? If you open %AppData%\Notepad++\config.xml (or, if you are using local config, then your c:\program files (x86)\notepad++\ directory, or wherever you installed notepad++), there should be a line that says something like:
<GUIConfig name="noUpdate" intervalDays="15" nextUpdateDate="20180227">yes</GUIConfig>
If it says “yes”, then it should be doing “noUpdate”, so it shouldn’t be auto-updating. If it says “no”, then it should be doing the update. (reverse logic in the config.xml compared to the state of the toggle switch in the preferences)
If all the copies of config.xml say “yes” to noUpdate, and if the GUI’s preferences shows the auto-updater is disabled, and it’s still trying to update, you could try to rename the gup.exe and possibly gup.xml in your c:\program files (x86)\notepad++\updater\ (or equivalent) directory