### 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)

"""View to show records from XCom table."""
    route_base = "/xcom"
    list_title = "List XComs"
    datamodel = AirflowModelView.CustomSQLAInterface(XCom)
    class_permission_name = permissions.RESOURCE_XCOM
    method_permission_name = {
        "list": "read",
        "delete": "delete",
        "action_muldelete": "delete",
    }
    base_permissions = [
        permissions.ACTION_CAN_CREATE,
        permissions.ACTION_CAN_READ,
        permissions.ACTION_CAN_DELETE,
        permissions.ACTION_CAN_ACCESS_MENU,
    ]
    search_columns = ["key", "value", "timestamp", "dag_id", "task_id", "run_id", "execution_date"]
    list_columns = ["key", "value", "timestamp", "dag_id", "task_id", "run_id", "map_index", "execution_date"]
    base_order = ("dag_run_id", "desc")
    base_filters = [["dag_id", DagFilter, list]]
    formatters_columns = {
        "task_id": wwwutils.task_instance_link,
        "timestamp": wwwutils.datetime_f("timestamp"),
        "dag_id": wwwutils.dag_link,
        "map_index": wwwutils.format_map_index,
        "execution_date": wwwutils.datetime_f("execution_date"),
    }
    @action("muldelete", "Delete", "Are you sure you want to delete selected records?", single=False)
    def action_muldelete(self, items):