Why "login items" notifications pop up while there's no app listed on startup or background?

Good to hear!

Applications or programs, especially not downloaded from the App Store, aren’t just removed from moving from the Apps folder to the Trash......as you’ve seen.

The best way, for the others here, is to utilize the un-installation instructions provided by the developer of the software, if available. However if the issues remain, the two locations you checked are where these apps store key components.

Other locations, particularly in the /Macintosh HD/Library is to check for the name of the app or developer in these locations, delete them and restart, (If of course deleting from /Applications, or using their uninstall instructions didn’t work:

Application Support

Extensions

Internet Plugins

Launch Agents

Launch Daemons

Scripting Additions

Staged Extensions

Startup Items

This is normally not needed, especially if truly uninstalled, and Mac is up to date, as well any any signed software, but I think the developers for these third party (Non-Apple) applications have to update their code to work with the ever-strict, but necessary Apple software.

In my opinion, it’s a small price to pay for this service. However I’m sure if Apple is aware of this notification type problem, and it isn’t completely necessary, they would fix it, however I like being notified when any Application starts running in the background every time I just log in. This gives the end user even more control and transparency.

If you truly would like to notify Apple of your concerns, I would contact them directly, they aren’t to get a hold of by phone:

Contact Apple for support and service - Apple Support