I have a custom theme which inherits from blank and I would like to override navigation-menu.js options how would I do that?
you can override navigation-menu.js into your theme and you can changes as per your requirement.
path for override js,
After override you have to just deploy command to see changes on frontend.
pub/static/frontend folder and deploy below command.
php bin/magento setup:static-content:deploy
Remove var folder. Check again.