This really is somewhat a subjective question.
Observed styles like thematic and carrington use hooks to show their styles.
Trying to puzzle out which works well with a far more efficient workflow.
Which appears more effective at theming? Attempting to weigh within the cons and pros of hooks versus. just including static files.
Hooks and can include()s are actually meant for two different reasons. Includes statically bring additional content to your theme, while hooks allow plug ins as well as your theme's functions.php to include content on-the-fly. Using the new-ant inclusions in WordPress of child styles, hooks also allow stated children to include content for your theme without modifying the core files.
All-in-all, this will make your theme more future-proof along with a much simpler recommendation when the time comes to think about theme frameworks to base a website upon.
If you use Thesis, this wordpress plugin WordPress › Thesis OpenHook « WordPress Plugins is extremely interesting from the hook perspective and what may be completed with other frameworks for clients and designers.
Go ahead and, make use of the hooks. This really is more effective, and enables your theme to experience nice with a number of icons and add-inches which rely on web site hooks. Using static includes can make your template a smaller amount flexible overall, and opens you as much as possible breakage as changes are created to the WordPress after sales.