### 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)

x_axis_date=True,
            x_axis_format=LINECHART_X_AXIS_TICKFORMAT,
            height=chart_height,
            chart_attr=self.line_chart_attr,
        )
        tis = dag.get_task_instances_before(base_date, num_runs, session=session)
        for task in dag.tasks:
            y_points = []
            x_points = []
            for ti in tis:
                if ti.task_id != task.task_id:
                    continue
                dttm = wwwutils.epoch(ti.execution_date)
                x_points.append(dttm)
                
                y_points.append(ti.prev_attempted_tries)
            if x_points:
                chart.add_serie(name=task.task_id, x=x_points, y=y_points)
        max_date = max((ti.execution_date for ti in tis), default=None)
        chart.create_y_axis("yAxis", format=".02f", custom_format=False, label="Tries")
        chart.axislist["yAxis"]["axisLabelDistance"] = "-15"
        session.commit()
        form = DateTimeWithNumRunsForm(
            data={
                "base_date": max_date or timezone.utcnow(),
                "num_runs": num_runs,
            }
        )
        chart.buildcontent()
        return self.render_template(