### 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)

qry = session.execute(
            select(
                final_task_instance_query_result.c.dag_id,
                final_task_instance_query_result.c.state,
                final_task_instance_query_result.c.is_dag_running,
                sqla.func.count(),
            )
            .group_by(
                final_task_instance_query_result.c.dag_id,
                final_task_instance_query_result.c.state,
                final_task_instance_query_result.c.is_dag_running,
            )
            .order_by(
                final_task_instance_query_result.c.dag_id,
                final_task_instance_query_result.c.is_dag_running.desc(),
            )
        )
        data = get_task_stats_from_query(qry)
        payload: dict[str, list[dict[str, Any]]] = collections.defaultdict(list)
        for dag_id in filter_dag_ids:
            for state in State.task_states:
                count = data.get(dag_id, {}).get(state, 0)
                payload[dag_id].append({"state": state, "count": count})
        return flask.json.jsonify(payload)
    @expose("/last_dagruns", methods=["POST"])
    @auth.has_access(
        [
            (permissions.ACTION_CAN_READ, permissions.RESOURCE_DAG),
            (permissions.ACTION_CAN_READ, permissions.RESOURCE_DAG_RUN),
        ]