Microsoft released a new Office 365 App Launcher version (version 3). Beside a massive experience change Microsoft also changes some stuff in the backend.
All info about the new experience can be found in this Microsoft post: New Office 365 app launcher and Office.com help you be more productive on the web
The “old” App Launcher needs an Exchange Online subscription for each user to let a user personalize his App Launcher. This was because of the App launcher settings are stored in the user mailbox. The settings are located in the PR_ROAMING_DICTIONARY property of the IPM.Configuration.Suite.Storage at the root folder of the mailbox. All this is based on JSON. The settings are located in Suite/AppsCustomizationDataTEST value and the property is called PinnedApps.
Scott Bueffe posted a detail description about this here: How to pin custom app tiles on behalf of your users in Office 365
With the new version Microsoft changed the way this information is stored. It is no longer located in a user’s Exchange Mailbox. Actually, we do not have any documentation about where the settings are stored now.
In fact, a user did not longer need an Exchange Online mailbox to customize the default Apps in his App Launcher.