### 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)

"""
        Returns a robots.txt file for blocking certain search engine crawlers.
        This mitigates some of the risk associated with exposing Airflow to the public
        internet, however it does not address the real security risks associated with
        such a deployment.
        """
        return send_from_directory(get_airflow_app().static_folder, "robots.txt")
    @expose("/audit_log")
    @auth.has_access(
        [
            (permissions.ACTION_CAN_READ, permissions.RESOURCE_DAG),
            (permissions.ACTION_CAN_READ, permissions.RESOURCE_AUDIT_LOG),
        ]
    )
    def legacy_audit_log(self):
        """Redirect from url param."""
        return redirect(url_for("Airflow.audit_log", **sanitize_args(request.args)))
    @expose("/dags/<string:dag_id>/audit_log")
    @auth.has_access(
        [
            (permissions.ACTION_CAN_READ, permissions.RESOURCE_DAG),
            (permissions.ACTION_CAN_READ, permissions.RESOURCE_AUDIT_LOG),
        ]
    )
    @provide_session
    def audit_log(self, dag_id: str, session: Session = NEW_SESSION):