A good rule of thumb for tagging on AO3:
Relationship tags are for searching.
For any ship that isn’t central to the fic, ask yourself:
If I were searching specifically for this ship, is there a decent probability that I would be interested this result? If not, it probably doesn’t need to be tagged.
If you feel that you need to warn for a background ship, you can always tag “Untagged Background Relationships” and then if you want you can specify what they are in the author’s notes. Search results are more accurate, you’ve covered your bases, everyone’s happy.
Relationship tags are for searching. If you need to warn for a background or briefly-mentioned ship, there are other ways to do it.
All of this is very true for character tags, too.