
Replying to myself here, just in case it's useful for someone else in the future, this is not elegant and I'm sure there are much better ways, but I am not a developer and it worked for me:
beans_modify_action_callback( 'beans_modify_menu_args', 'your_theme_modify_menu_args' );
function your_theme_modify_menu_args( $args ) {
// contents of beans_modify_menu_args with any modifications for your theme
// (see https://github.com/Getbeans/Beans/blob/release/1.5.0/lib/render/menu.php)
// in my case, I deleted the line specifying data-uk-nav for offcanvas menus
}