Meta Boxes: ‘admin_init’ or ‘add_meta_boxes’ hook?

Have a look at this list: http://codex.wordpress.org/Plugin_API/Action_Reference

1. It doesn’t matter which one you use as long as it’s not too early and not too late. It’s best to use intuitive and predictable hooks, so add_meta_boxes is preferred. Someday in the future WordPress may change something and by using the most appropriate hooks you increase your chances that your code will still work in the future.
2. There is one exception that I can think of to that. Sometimes (in cases that are very unlikely to happen) you may need to for instance call add_theme_support() which is generally used with after_setup_theme action hook only for logged in users that are administrators but this hook doesn’t allow you to access this information yet. You would therefore have to probably use set_current_user or init action hooks instead (after doing some research if it’s safe to do that).