Does Jonas have freckles or any other type of distinct feature?

Not that we are told, no. In fact, Lois Lowry really doesn't describe Jonas. This might be due to the point of view the book is written in, which is the third person limited. This means that we know all of the protagonist's (Jonas) thoughts and actions, but no one else's. As a result, Jonas really had no reason to notice his own appearance and comment on it.

That alone tells us something because if...

Not that we are told, no. In fact, Lois Lowry really doesn't describe Jonas. This might be due to the point of view the book is written in, which is the third person limited. This means that we know all of the protagonist's (Jonas) thoughts and actions, but no one else's. As a result, Jonas really had no reason to notice his own appearance and comment on it.

That alone tells us something because if Jonas DID have freckles, it probably would have been mentioned since freckles would be something that would make him unique. Since he lives in a society that has adopted Sameness where different colored hair and eyes are rare, we probably would have been told about freckles.

The only physical trait that seems unique about Jonas is his eye color. We know his eyes are fair and we get the impression they are probably blue. This is mentioned multiple times. We also know the Giver's eyes and Gabriel's eyes are the same color, which is interesting because each of these characters have the ability to share and receive memories.