Ontologies only built with classes and not class instances

I am wondering why public biomedical ontologies are often organized in such a way that there are no class instances and only classes? I understand it in a way that all instances are classes, but I do not understand what is the advantage or purpose of such modelling? Those classes have also only annotation properties. For example NCIT ontology: https://bioportal.bioontology.org/ontologies/NCIT/?p=summary. I would appreciate if someone could provide me with an explanation what is the purpose of such model and if there is an advantage to a model where classes have class instances. I am definitively not an expert in the field and I only was working on modelling 'standard' ontologies with classes and their instances.

TLDR

The reason for preferring classes over individuals (or instances) is that classes allow for sophisticated reasoning which is used to infer classification hierarchies.

The longer answer

The semantics of OWL allows you to make the following type of statements:

1. ClassExpression1 is a subclass of ClassExpression2
2. PropertyExpression1 is a subproperty of PropertyExpression2
3. Individual c1 is an instance of Class1
4. Individual x is related to individual y via property1

Of these 4 options, (1) by far allows for the most sophistication. Intuitively it comes down to how much each of these allow you to express and the reasoning capability to derive inferences from those statements. To get an intuitive feel of this, using the OWL Direct Semantics, we can see what ClassExpression1 and ClassExpression2 can be substituted with:

There no way that this expressivity can be achieved using individuals.

Individuals vs Classes

In your question you say that all instances (individuals) are classes. This is not exactly true. Rather, classes consists of instances or instances belong to classes. From a mathematical perspective classes are sets and individuals are members of a set.

Annotations in biomedical ontologies

These ontologies have a substantial (80%-90%) amount of annotations. However, they do have lots of logical axioms. You can see it for example when you look at http://purl.obolibrary.org/obo/NCIT_C12392 on the righthandside, if you scroll down to the bottom, you will see the axioms listed: