refactor: select in workflow_tools_manage_service

[RenzoMXD]

Summary

• Migrate all 10 db.session.query() calls to SQLAlchemy 2.x select() style in workflow_tools_manage_service.py
• Replace .first() with db.session.scalar() + .limit(1) for single-row queries
• Replace .query().where().delete() with db.session.execute(delete().where())

Test plan

• All 79 unit tests pass for tools service tests
• Type checks pass (basedpyright + pyrefly + mypy)

Part of #22668

[github-actions]

Pyrefly Diff

No changes detected.

[RenzoMXD]

Review please. @asukaminato0721