sono hutago ha kao dake de naku, koe mo yoku nite imasu.

は marks the topic of the sentence. It sets up その双子 as what the sentence is about.

So the sentence has a structure like:

As for those twins, not only their faces, but their voices too, resemble each other closely.

This is the pattern Aだけでなく、Bも, which means not only A, but also B.

Here:

• 顔だけでなく = not only their faces
• 声も = their voices too / also their voices

So the sentence is contrasting two things and saying both are similar.

In patterns like Nだけでなく, it is very common for the noun to come directly before だけ with no extra particle.

So 顔だけでなく is a natural way to say not only the face / not only in appearance.

If a particle were added, the nuance or phrasing would shift a little, but the version here is completely standard and natural.

Japanese often leaves out possessives like their, his, or her when they are obvious from context.

Since その双子 is already the topic, 顔 and 声 are naturally understood as the twins’ faces and the twins’ voices. This is especially common with body parts and personal attributes.

It can be understood a little more broadly than just the physical face. In this kind of sentence, 顔 often means facial appearance or how someone looks in the face.

So 顔が似ている can feel like:

• their faces look alike
• they look alike facially

Yes, よく can mean often, but here it does not.

With 似ている, よく usually means something like:

• closely
• very much
• quite a lot

So よく似ています means resemble each other closely or are very similar. It is not talking about frequency.

The usual way to say that things or people resemble each other is 似ている. This describes a current state of similarity.

So:

• 似ている = be resembling / be similar
• 似ています = polite form of 似ている

似ます exists, but when talking about how people look or sound alike, 似ています is much more natural.

Normally, yes. A full pattern is:

AはBに似ている = A resembles B

But here, B is omitted because it is obvious. Since the topic is the twins, the natural meaning is that the twins resemble each other.

Japanese often leaves out information that the listener can easily infer, so there is no need to spell out each other or add another noun after に in this sentence.