Why is „Favorites“ popup in iPad’s Safari half empty?

It’s possible that your “Favourites” aren’t necessarily being saved where you think you’re saving them...

I recommend that you begin with reviewing this section of the iPad User Guide for iPadOS:

https://support.apple.com/en-gb/guide/ipad/ipadc602b75b/ipados

Now, your Bookmarks (Favourites) have a considerably more complex hierarchy and structure than is immediately obvious...

When you tap the “+” icon to open a new tab, the page of Favourites icons that appears will only show you the contents of the Favourites folder - which is not the “top level” or “root” of the Bookmarks folder-structure.

To the left of the Address Bar, you’ll see a small open-book icon; tap this icon to reveal a sidebar - the icon with be highlighted in blue (NB - a further tap of the icon will close the sidebar - and the icon will lose its blue highlight).

With the sidebar open, you can view the currently selected Bookmarks folder (e.g., Favourites), the Reading List or History. You can select from these three options using the three associated icons (in order - an open-book, glasses and a clock-face). Tap the left open-book icon to show the Bookmarks/Favourites sidebar.

Having exposed the Bookmarks/Favourites list, you’ll notice that a navigation button has now appeared at top-left of the sidebar (it may be annotated as Back or All) - unless you are already at the root level. If not already at the top “root” level, tap the navigation button until you reach the root - when the navigation button will disappear.

At the top of this list is a Favourites folder - labelled with a ⭐️. By default, it is the contents of this folder that will appear in the list of Favourites that appears when you open a new tab! You can create other folders - or directly save a Favourite in the top-level root folder. These folders and saved Favourites can be edited or moved using the Edit button that you’ll see at the bottom-right of the sidebar.

Take some time to explore this structure and the editing features - you’ll note that from the edit option you can similarly navigate the folder structure, rename or edit an item, move an item in the listing using the drag-bar that appears next to each item, or delete. Tap Done to finish editing.

The actual folder in this hierarchy in which your Favourites are saved can be configured in Settings:

Settings > Safari > Favourites - select the folder from the list - the full folder structure is presented.

You need to be mindful that this setting determines precisely where a Favourite will be saved in the Bookmarks folder hierarchy!

I hope this explanation provides some helpful insight and clarity. Bookmarks management, if you deviate from default settings, can be a whole lot more complex than is immediately obvious.

I hope this information provides the information you need to resolve the unexpected observed behaviour.