### 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)

base_date = dag.get_latest_execution_date() or timezone.utcnow()
        with create_session() as session:
            query = select(DagRun).where(DagRun.dag_id == dag.dag_id, DagRun.execution_date <= base_date)
        run_type = request.args.get("run_type")
        if run_type:
            query = query.where(DagRun.run_type == run_type)
        run_state = request.args.get("run_state")
        if run_state:
            query = query.where(DagRun.state == run_state)
        dag_runs = wwwutils.sorted_dag_runs(
            query, ordering=dag.timetable.run_ordering, limit=num_runs, session=session
        )
        encoded_runs = [wwwutils.encode_dag_run(dr, json_encoder=utils_json.WebEncoder) for dr in dag_runs]
        data = {
            "groups": dag_to_grid(dag, dag_runs, session),
            "dag_runs": encoded_runs,
            "ordering": dag.timetable.run_ordering,
        }
        
        return (
            htmlsafe_json_dumps(data, separators=(",", ":"), dumps=flask.json.dumps),
            {"Content-Type": "application/json; charset=utf-8"},
        )
    @expose("/object/historical_metrics_data")
    @auth.has_access(
        [
            (permissions.ACTION_CAN_READ, permissions.RESOURCE_CLUSTER_ACTIVITY),
        ]
    )
    def historical_metrics_data(self):