### Apache Airflow version

2.7.0

### What happened

On the DAGs page, the All, Active, and Paused counts include deleted DAGs. This is different from <= 2.6.1 (at least), where they were not included in the totals. Specifically this is for DAGs for which the DAG files have been removed, not DAGs that have been deleted via the UI.

### What you think should happen instead

Including deleted DAGs in those counts is confusing, and this behavior should revert to the previous behavior.

### How to reproduce

Create a DAG. 
Wait for totals to increment.
Remove the DAG file.

The totals will not change.

### Operating System

Debian GNU/Linux 11 (bullseye)

### Versions of Apache Airflow Providers

```apache-airflow-providers-amazon==8.5.1
apache-airflow-providers-celery==3.3.2
apache-airflow-providers-cncf-kubernetes==7.4.2
apache-airflow-providers-common-sql==1.7.0
apache-airflow-providers-datadog==3.3.1
apache-airflow-providers-elasticsearch==5.0.0
apache-airflow-providers-ftp==3.5.0
apache-airflow-providers-google==10.6.0
apache-airflow-providers-http==4.5.0
apache-airflow-providers-imap==3.3.0
apache-airflow-providers-microsoft-azure==6.2.4
apache-airflow-providers-postgres==5.6.0
apache-airflow-providers-redis==3.3.1
apache-airflow-providers-salesforce==5.4.1
apache-airflow-providers-slack==7.3.2
apache-airflow-providers-snowflake==4.4.2
apache-airflow-providers-sqlite==3.4.3
```

### Deployment

Astronomer

### Deployment details

_No response_

### Anything else

I suspect the issue is with [DagModel.deactivate_deleted_dags](https://github.com/apache/airflow/blob/f971ba2f2f9703d0e1954e52aaded52a83c2f844/airflow/models/dag.py#L3564), but I'm unable to verify.



### Are you willing to submit PR?

- [ ] Yes I am willing to submit a PR!

### Code of Conduct

- [X] I agree to follow this project's [Code of Conduct](https://github.com/apache/airflow/blob/main/CODE_OF_CONDUCT.md)

owners_query = owners_query.where(DagModel.is_paused)
        filter_dag_ids = get_airflow_app().appbuilder.sm.get_accessible_dag_ids(g.user)
        dag_ids_query = dag_ids_query.where(DagModel.dag_id.in_(filter_dag_ids))
        owners_query = owners_query.where(DagModel.dag_id.in_(filter_dag_ids))
        payload = [
            row._asdict()
            for row in session.execute(dag_ids_query.union(owners_query).order_by("name").limit(10))
        ]
        return flask.json.jsonify(payload)
class DagDependenciesView(AirflowBaseView):
    """View to show dependencies between DAGs."""
    refresh_interval = datetime.timedelta(
        seconds=conf.getint(
            "webserver",
            "dag_dependencies_refresh_interval",
            fallback=conf.getint("scheduler", "dag_dir_list_interval"),
        )
    )
    last_refresh = timezone.utcnow() - refresh_interval
    nodes: list[dict[str, Any]] = []
    edges: list[dict[str, str]] = []
    @expose("/dag-dependencies")
    @auth.has_access(
        [
            (permissions.ACTION_CAN_READ, permissions.RESOURCE_DAG_DEPENDENCIES),
        ]
    )
    @gzipped
    @action_logging
    def list(self):