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I agree with 1 out of 2. Just because an ID is in the theme does not mean that it needs an explicit CSS style defined for it.
As an application and theme developer, I prefer to add hooks to the html elements liberally, so that I'm not focused on the visual design of the document, but rather its logical grouping.
In the default theme I think this is even more important of a practice, as it will be used as a template for many user-created themes. Having those hooks already in the html makes the CSS customization MUCH easier.
Of course, a compromise might be adding a blank style for that id to the theme:
#headerlogo {}