Jordan Dayton requested that I post this here. Honestly, it feels sort of odd to write an entire blog post about a single API endpoint, but here goes.
When installing External Tools (aka Apps, aka LTI tools), especially from commercial publishers, you will often find that the resulting course menu items appear active by default. That's fine, even preferred, when an instructor installs the app in a single course. However, when an admin installs such an app at the account or sub-account level, you generally want it to appear disabled by default. Otherwise it will appear in every course menu in the account, and in most cases, need to be disabled manually. Currently there is no easy way to correct this. Admins can not control the default availability of course links. If, like me, you wish you could, please go vote for Allow account admins to set default course navigation menu.
In the meantime, the only way I know of to disable the links by default is to hit the edit external tool API endpoint: