I'm wondering what is the use of the wp_links table, couldn't links have been implemented as a custom post type, if the menu system also uses custom post types?


In short YES, they could have. As anything else could have been implemented as custom post type and/or custom taxonomy.

But WordPress is a grown system - now 9 years old - and things are moving slowly to keep most stuff backwards compatible.

In short, with WP 3.5, the Links Manager will be moved to a plugin, as you can read in the trac ticket.

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