### 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)

cum_chart = nvd3.lineChart(
            name="cumLineChart",
            x_custom_format=True,
            x_axis_date=True,
            x_axis_format=LINECHART_X_AXIS_TICKFORMAT,
            height=chart_height,
            chart_attr=self.line_chart_attr,
        )
        y_points = defaultdict(list)
        x_points = defaultdict(list)
        task_instances = dag.get_task_instances_before(base_date, num_runs, session=session)
        if task_instances:
            min_date = task_instances[0].execution_date
        else:
            min_date = timezone.utc_epoch()
        ti_fails = (
            select(TaskFail)
            .join(TaskFail.dag_run)
            .where(
                TaskFail.dag_id == dag.dag_id,
                DagRun.execution_date >= min_date,
                DagRun.execution_date <= base_date,
            )
        )
        if dag.partial:
            ti_fails = ti_fails.where(TaskFail.task_id.in_([t.task_id for t in dag.tasks]))
        ti_fails = session.scalars(ti_fails)
        fails_totals: dict[tuple[str, str, str], int] = defaultdict(int)
        for failed_task_instance in ti_fails:
            dict_key = (