Dear @JPache,
Thank you for posting your question in the Microsoft Q&A forum.
I understand how inconvenient it must be to open the Change the look panel and find that the Navigation option is missing when you expected to switch between Horizontal and Vertical layouts. I appreciate your patience while looking into this.
From my test environment, the Navigation setting normally remains available in modern SharePoint sites. However, there are specific conditions where this option disappears. Based on what you described, it is very likely related to the SharePoint Server Publishing Infrastructure feature or hub site behavior.

When the SharePoint Server Publishing Infrastructure (classic publishing) feature is enabled at the site collection level, the modern Navigation and Footer controls are suppressed. This is common after migrating or importing classic content into a modern site. With this feature active, only Theme, Header, and a few other options remain visible.
In some cases, hub-connected sites may also temporarily hide the navigation settings. Unlinking and linking again can refresh the panel and restore the options.
Below are two possible paths depending on whether your site must continue using classic publishing.
Option 1: Deactivate the Classic Publishing Infrastructure
If your site no longer depends on classic publishing features, you can deactivate it. This usually restores the modern Navigation controls immediately.
Notes:
- This step requires Full Control permissions to proceed.
- Additionally, deactivating the publishing feature may disable classic functionalities that your site might still rely on. If this applies to your environment, I recommend testing the change in a safe environment before applying it to production.
Go to Site Settings (Site Information > View all site settings).

Under Site Collection Administration, select Site collection features.

Locate SharePoint Server Publishing Infrastructure.
Select Deactivate > Refresh the site.

Open Settings > Change the look and check whether Navigation is now visible.
Option 2: Keep Classic Publishing enabled
If your site must continue using classic publishing features, the modern Navigation panel will remain hidden. Microsoft recommends modernizing sites rather than running modern pages with classic publishing enabled, as the two systems are not fully compatible.
If the classic feature cannot be removed, consider using or creating a fully modern Communication or Team site for consistent modern navigation.
Option 3: If the site is associated with a hub, you can try refreshing the hub connection:
Go to Site Settings.
Select Hub site association.
Choose Unlink from hub.
Open Settings > Change the look again to check if Navigation returns.
If it appears, set your preferred orientation.
Re‑associate the site with the hub afterwards.
This helps in cases where hub metadata temporarily blocks the panel from showing all available options.
This article provides further guidance on the topic: Remove a hub site - SharePoint in Microsoft 365 | Microsoft Learn
Additional information is available in the following resources:
Why move from publishing sites to communication sites? - SharePoint - SharePoint in Microsoft 365 |…
Features enabled in a SharePoint publishing site - Microsoft Support
Change the look of your SharePoint site - Microsoft Support
Customize the navigation on your SharePoint site - Microsoft Support
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I hope this information is helpful. If you have any questions or need further support, please don’t hesitate to reach out at any time.
Thank you for your patience and understanding.
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