### 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)

TaskInstance.dag_id == dag.dag_id,
            TaskInstance.run_id.in_([dag_run.run_id for dag_run in dag_runs]),
        )
        .group_by(TaskInstance.task_id, TaskInstance.run_id, TaskInstance.state, TaskInstance._try_number)
        .order_by(TaskInstance.task_id, TaskInstance.run_id)
    )
    grouped_tis = {task_id: list(tis) for task_id, tis in itertools.groupby(query, key=lambda ti: ti.task_id)}
    sort_order = conf.get("webserver", "grid_view_sorting_order", fallback="topological")
    if sort_order == "topological":
        def sort_children_fn(task_group):
            return task_group.topological_sort()
    elif sort_order == "hierarchical_alphabetical":
        def sort_children_fn(task_group):
            return task_group.hierarchical_alphabetical_sort()
    else:
        raise AirflowConfigException(f"Unsupported grid_view_sorting_order: {sort_order}")
    def task_group_to_grid(item, grouped_tis, *, is_parent_mapped: bool):
        if not isinstance(item, TaskGroup):
            def _get_summary(task_instance):
                return {
                    "task_id": task_instance.task_id,
                    "run_id": task_instance.run_id,
                    "state": task_instance.state,
                    "queued_dttm": task_instance.queued_dttm,
                    "start_date": task_instance.start_date,
                    "end_date": task_instance.end_date,
                    "try_number": wwwutils.get_try_count(task_instance._try_number, task_instance.state),
                    "note": task_instance.note,
                }
            def _mapped_summary(ti_summaries):