System - Akeeba GeoIP provider plugin. Yes, you need to remove it manually. This plugin had never been part of Admin Tools itself. It's a separate plugin which provided shared functionality for our extensions (and possibly some third party extensions as well). That's why it's not auto-removed.
System - Admin Tools Update Email. This is NOT the plugin you think it is. This plugin sends you an email about available updates for Admin Tools itself. However, we have not included this plugin for several releases and it's safe to remove.
FYI the System - Admin Tools Joomla! update email plugin is automatically uninstalled when you install Admin Tools 5.5.0. We have made the obsolete plugins uninstallation code part of our framework library (FOF), making it practical to now uninstall obsolete plugins when you install a new version which no longer needs or supports them.
However, to avoid messing up your sites, we only remove plugins which we are absolutely certain are not used by anything else. This is not the case with the System - Akeeba GeoIP provider plugin since it's not part of Admin Tools itself and it was used beyond just Admin Tools. That's actually this was extracted to its own plugin when it was previously –many years ago– part of Admin Tools itself. This plugin is not safe to remove unless you have updated all of our software, especially if some of our extensions in use were releases before 2015 when we started always doing checks to see if the plugin is installed as opposed to trusting that if you enable an IP geolocation feature you have already enabled this plugin.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!