Most other apps are pretty good at recognizing this app's hidden items. It's a simple metafield that needs to be excluded. We've notified most other apps that this might effect, but since new apps are added everyday, you should confirm that none of your other apps see or use the hidden variants. Since we don't have any control of how other apps that aren't our own function, we aren't able to prevent other apps from seeing and using these variants.
If you're technical, here are the attributes for the products you'll want to exclude:
"key" => "ShappifyHidden",
"value_type" => "string",
"namespace" => "inventory",
"value" => "true"