Answered
Why can't I delete a Pantone Swatch color in Illustrator?
When I select this color from the Swatches panel, the "Delete Swatch" icon is greyed out.


Turns out I have placed links (Photoshop format) that have Pantone colors in them (through channels), so the Pantones were automatically imported into Illustrator, and that's why you cannot delete them, unless you delete those links, or you delete the Pantone from within the PSD links.
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