### 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)

owner_links_dict = DagOwnerAttributes.get_all(session)
            import_errors = select(errors.ImportError).order_by(errors.ImportError.id)
            if (permissions.ACTION_CAN_READ, permissions.RESOURCE_DAG) not in user_permissions:
                
                import_errors = import_errors.join(
                    DagModel, DagModel.fileloc == errors.ImportError.filename
                ).where(DagModel.dag_id.in_(filter_dag_ids))
            import_errors = session.scalars(import_errors)
            for import_error in import_errors:
                flash(
                    f"Broken DAG: [{import_error.filename}] {import_error.stacktrace}",
                    "dag_import_error",
                )
        from airflow.plugins_manager import import_errors as plugin_import_errors
        for filename, stacktrace in plugin_import_errors.items():
            flash(
                f"Broken plugin: [{filename}] {stacktrace}",
                "error",
            )
        num_of_pages = math.ceil(num_of_all_dags / dags_per_page)
        state_color_mapping = State.state_color.copy()
        state_color_mapping["null"] = state_color_mapping.pop(None)
        page_title = conf.get(section="webserver", key="instance_name", fallback="DAGs")
        page_title_has_markup = conf.getboolean(
            section="webserver", key="instance_name_has_markup", fallback=False
        )
        dashboard_alerts = [
            fm for fm in settings.DASHBOARD_UIALERTS if fm.should_show(get_airflow_app().appbuilder.sm)
        ]
        def _iter_parsed_moved_data_table_names():