### 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)

from flask_appbuilder import BaseView, ModelView, expose
from flask_appbuilder.actions import action
from flask_appbuilder.models.sqla.filters import BaseFilter
from flask_appbuilder.security.decorators import has_access
from flask_appbuilder.urltools import get_order_args, get_page_args, get_page_size_args
from flask_appbuilder.widgets import FormWidget
from flask_babel import lazy_gettext
from jinja2.utils import htmlsafe_json_dumps, pformat  
from markupsafe import Markup, escape
from pendulum.datetime import DateTime
from pendulum.parsing.exceptions import ParserError
from sqlalchemy import Date, and_, case, desc, func, inspect, select, union_all
from sqlalchemy.exc import IntegrityError
from sqlalchemy.orm import Session, joinedload
from wtforms import BooleanField, validators
import airflow
from airflow import models, plugins_manager, settings
from airflow.api.common.airflow_health import get_airflow_health
from airflow.api.common.mark_tasks import (
    set_dag_run_state_to_failed,
    set_dag_run_state_to_queued,
    set_dag_run_state_to_success,
    set_state,
)
from airflow.configuration import AIRFLOW_CONFIG, conf
from airflow.datasets import Dataset
from airflow.exceptions import (
    AirflowConfigException,
    AirflowException,
    AirflowNotFoundException,