Is there any benefit to a retagging project here? Do we just try to use it more going forward? Do we even care?
No need to fix what's not broken
Bonus action questions and answers do not exist in a vacuum. They are associated with a wide variety of things in D&D 5e across a wide variety of classes, skills, spells, feats, monsters, etc. The key issue will be something that has bonus action, but it's the feature, the class, the monster, or the feat that is what matters. It is those features (etc) that matter in terms of the 'optimization' and 'Does it work like I think it does?' questions. With that in mind, the tag is fine as is. We need not require anyone to use it, and, it's there if needed by the question's asker.
I've been on this site for about five years. I fail to see any site problem that this tag has caused. I have seen some problems that other tags have caused, so I'll close by saying: there isn't a problem to fix.
Let it ride.
I am not sure how to say this last thought, but here goes: I am not comfortable with the meta/community taking a stance of "we need to use this tag more" - not sure why I feel this way, but it just doesn't feel right.
Lots of questions using the phrase “bonus action” without using bonus-action is, to me, entirely expected and normal. After all, lots of things use bonus actions, which may well be mentioned in questions about those things (particularly if the rules specifying their use are quoted), without the question being about any bonus action or the rules for bonus actions or how bonus actions work or whatever. If a question is asking “this thing is a bonus action, does that mean I can use it at the same time as that other thing?” then yeah, it should probably have bonus-action. But if it’s “this thing says ‘as a bonus action, you can summon a thingamabob,’ how do thingamabobs work?” then it absolutely should not have bonus-action.
And, prima facie, I would guess that there are vastly more questions for the latter sort than there are of the former sort. Your numbers confirm that expectation. Seems like the tag is probably mostly used more-or-less correctly.
It looks like a few of the questions that don't feature the bonus-action tag do have the actions tag. This makes sense to me since bonus actions are actions. This is reinforced on page 6 of the Sage Advice Compendium:
Does using a bonus action break invisibility from a warlock’s One with Shadows invocation?
Taking a bonus action breaks the invisibility of a warlock’s One with Shadows. A bonus action is an action.
I'm not sure if there's a way to filter by the tag count but a quick glance through the first page shows that only a small number of these have reached the five tag cap which would prevent the bonus-action tag from being appended. So most would be fixable.
I think one of the main benefits of the tags is that it allows users who are wanting to learn about a topic to focus their search results fairly easily. To that end, I think there it is worth adding the tag on when there's room.