How to remove "Help us keep magento healthy" in Magento 2.1

It is in two places:

• in vendor/magento/module-theme/view/frontend/templates/html/footer.phtml as you said
• but also in vendor/magento/module-theme/view/frontend/templates/html/bugreport.phtml

Regarding the second one you can remove the entire block with the following layout code:

<referenceBlock name="report.bugs" remove="true" />