The MongoDB Certification team regularly checks and updates its question bank to make sure that the questions related to any deprecated methods are not asked. So, you can stay assured that you will not find yourself in a situation as you mentioned.
The syllabus ie. the breakdown of the topics and what to prepare for those topics are all listed in the Developer Exam Study Guide. Kindly prepare using this guide only.
Wishing you the best in your certification preparation! Feel free to reach out for anything else as well.
Practicing with case studies can be a helpful way to prepare for certification exams, as they provide a realistic scenario to which you can apply your knowledge. Be sure to review the official exam guide and take practice exams to gauge your readiness.