### 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)

.join(
                    subq_failed,
                    and_(
                        subq_all.c.dag_id == subq_failed.c.dag_id,
                        subq_all.c.start_date == subq_failed.c.start_date,
                    ),
                )
                .subquery()
            )
            failed_dags = dags_query.join(subq_join, DagModel.dag_id == subq_join.c.dag_id)
            is_paused_count = dict(
                session.execute(
                    select(DagModel.is_paused, func.count(DagModel.dag_id)).group_by(DagModel.is_paused)
                ).all()
            )
            status_count_active = is_paused_count.get(False, 0)
            status_count_paused = is_paused_count.get(True, 0)
            status_count_running = get_query_count(running_dags, session=session)
            status_count_failed = get_query_count(failed_dags, session=session)
            all_dags_count = status_count_active + status_count_paused
            if arg_status_filter == "active":
                current_dags = active_dags
                num_of_all_dags = status_count_active
            elif arg_status_filter == "paused":
                current_dags = paused_dags
                num_of_all_dags = status_count_paused
            elif arg_status_filter == "running":
                current_dags = running_dags
                num_of_all_dags = status_count_running
            elif arg_status_filter == "failed":