Exclude certain entries and its children from navigation
If it’s true that the descendantOf param doesn’t allow to pass in multiple entries, you probably need to work around that issue and grab the descendants for each parent entry individually.

{% set parentIds = [3, 4, 5] %}
{% set excludeIds = parentIds %}

{% for parentId in parentIds %}
    {% set ids = craft.entries.descendantOf(parentId).ids() %}
    {% set excludeIds = excludeIds|merge(ids) %}
{% endfor %}

{% set idParam = 'and, not ' ~ excludeIds|join(', not ') %}

{% set entries = craft.entries.section('pages').id(idParam) %}