Because system-admin rights are for doing system administration. Not "I can see/do everything" - that's a terrible permissions model, and thankfully one Atlassian stay away from.
As a system admin, I don't want to be able to see everything in a 5000 space, million page Confluence, I want to see the spaces that are relevant to me.
For the "invisible" spaces, check the permissions - you can still do that as an admin, even when you're not able to see the content.
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