What would dental schools think when a GPA started out really high, like 3.9, then start declining later on?

There is no definitive answer for this. Generally a downwards trend is not good. Even though classes may be getting harder an applicant is expected to maintain the same performance or improve on themselves.
In my opinion, it ultimately depends on the type of classes (and how many classes) the individual was taking when achieving the high GPA and comparing that to the type (and how many classes) were taken when the lower GPA was achieved. It is important to remember that the application review process is comprehensive. They are not only looking at your GPA but at your workload, extracurricular activities, and any issues you noted on the application like hospitalization.
Ultimately, maintaining the high GPA is ideal and a decline in GPA is expected to make an application less attractive than that with the high GPA. In some cases I honestly do not think it will hinder an application by much, if any.

How important are the prerequisite classes listed for dental school?

Prerequisite classes are most likely mandatory courses the school requires in order to be accepted in their school. Any class that is mandatory must be taken or listed on an AADSAS application. From what I understand, you will still be accepted to the school if the course is listed on your application, but you MUST complete the course before the dental school year begins. I am not sure exactly what happens if you fail to complete such a requirement, but I would imagine that the upcoming dental student may lose the spot in that dental school.
Dental schools also have recommended course lists. These are different than the required courses and completing them is optional, but highly recommended. Completing the recommended classes as as the required courses do improve your chances of getting in, but not taking them should not hurt your application. Taking these courses also puts one at an advantage during dental school. Many of the recommended courses are classes you will be taking during your first two years of dental school which is very similar to medical school. During these two years a dental student is taking around 30 units of classes at a time. Exposing oneself to the material during undergrad will free up time to study for other classes.
If you are still concerned about prerequisites, I would not trust anybody but an admissions representative from the school. From what I have seen, taking classes at a community college is okay but completion of the requirements at a four year university is heavily preferred. .

Am I waitlisted if I have not heard back from the school yet?

If you have not heard back from the school you are not waitlisted. The general rule is if you haven’t received a rejection then your application is still pending a decision. Waitlisting for dental school only occurs after interviews, not before. I would not worry too much if you haven’t heard back from dental schools by December. It is common and completely normal for interview offers to come in later than December! Not hearing back is the best situation to be in since most schools will notify you of a rejection almost immediately. You can check your individual application statuses on the AADSAS website.

What do you mean by apply early?

Applying early doesn’t mean just submitting your application. It means having your application 100% complete by the end of July. If any part of your application is missing, a school will put your application on hold and your application will not be evaluated until all the missing parts have arrived.

If the school is waiting for new DAT scores, they will get them shortly following the exam (approximately 3 weeks). Don’t worry! There will be plenty of spots left at every dental school. Many people submit their application in June prior to taking the DAT. It is a fairly common practice and as a result many people will be at the same stage.

If the school is waiting on letters of recommendation remind the writer that your application is already submitted and is currently on hold until all the components like the letter of recommendation are submitted. Do not pressure them! It was your responsibility to give them enough time to finish the letter.  Pressuring them will only result in a poorer letter or remarks finding their way into your letter.

I keep hearing apply early. What does “early” mean when it comes to submitting my application?

Generally, if you apply before the end of the month of July, you are considered an early applicant. Applications submitted during the first month month are immediately processed but not sent to dental schools until the last Friday of June as a single giant batch. Then applications are reviewed by dental schools and may start sending interview invites shortly after while other schools may wait until late September or early October (it varies for each dental school). As a result, submitting on the first day does not have a significant advantage over submitting at the end of June. Ultimately, you should submit as soon as you have everything ready. Every day can potentially help you get into your dream school!

There isn’t a distinct cut-off for what is defined as an early applicant. Think of it as a gradient throughout the cycle. The later it is in the cycle one submits, the less early an applicant is.