I found a little trick on how Outlook retrieves mail from Gmail and sort the labels into sub-folders. For that I created a [Gmail] label and nested every other label underneath.
It works for some labels - they show up in Outlook as a neat subfolder including the tagged mails. But others are just getting reverted to their old position, so instead of staying nested under [Gmail], they end up back on the same hierarchy level and thus don't show up in Outlook at all.
There seems no pattern to which labels stay and which get reverted either.
According to my research, you can configure a root folder for your Gmail account, as you are now working of the [Gmail] root folder in Outlook, you’ll see all your Labels directly under your main mailbox. To solve this, create another Label under the [Gmail] Label in the web interface and call it for instance “Labels”. Now you can make all your own Labels a nested Label of the Labels folder. And then create subfolders in Outlook and Labels in Gmail.
Specific steps refer to this article. Gmail IMAP – Solving the [Gmail] separation