https://github.com/barisusakli/nodebb-plugin-topic-noindex This is a plugin that does it for topics.
There is no built in way to do it in core. So to do it for categories you would have to fork and extend the above plugin.
Re: Disable/Remove "There are no topics in this category."
Using this simple CSS, I have turned all of my categories with subcategories into cosmetic categories only:
.subcategory+hr,
.subcategory~.clearfix,
.subcategory~.alert {display:none;}
There's a new setting for categories to be displayed as "sections" instead of true categories in the ACP. It's a per-setting category.