How to reference without tagging?
The pages that list content related to specific Taxonomy terms are created through views called Taxonomy term (usually at /admin/structure/views/view/taxonomy_term). 

You can control what those pages output by editing that Views. I usually disable that original View and Duplicate it to work on overrides, so I can always refer back to the original if something goes wrong. 

Which exact steps to take to exclude depends on your particular needs. 

If there aren't that many nodes that need to be excluded you can just add the filter for node ID, use the Is not equal to Operator and enter the ID of the node that is not supposed to be found on Taxonomy term pages. 

This solution will exclude that node from all the terms pages. If that node is referencing more than one term, it will not display on any of the terms pages. 

To exclude more than one node you can add as many ID filters as you need, or more conveniently use the Regular expression, see this answer for more info: How to exclude multiple nodes based on their ID in taxonomy term view?

If you need to exclude your list of nodes from terms from one Vocabulary, but not from all the other Vocabularies, you'd have to modify the Contextual filter settings in those Views and configure separate ones for that special vocabulary and then the other Contextual for all the rest. You'd have to use the OR instead of AND (there's a module for that). This requires a bit more experience with Views configuration. 



Another way may be to create a new field on your content, it probably makes the most sense to make it of type Boolean, that only have true/false states, and set those special nodes to True for that field (hide that field on Manage display, this is just your internal mark). Then in Taxonomy Views exclude the nodes that have that field set to True. 

The advantage of this approach is that you control that when creating/editing nodes, while in the above solution you have to go edit Views each time. 

Anything more than that you'd have to think about your site structure and change filters in Views to match that logic.