This is somewhat a subjective question.
Noticed themes like thematic and carrington use hooks to display their themes.
Trying to figure out which works best for a more efficient workflow.
Which seems more efficient at theming? Trying to weigh in the cons and pros of hooks vs. just including static files.
By all means, use the hooks. This is more efficient, and allows your theme to play nice with a variety of widgets and add-ins that also depend on the template hooks. Using static includes will make your template much less flexible overall, and opens you up to possible breakage as changes are made to the WordPress backend.