I think you also can use "他们”,because maybe there are several same shops located at the different area. So the sentence could be:这家商店很好的，他们的衣服不太贵。

you can use "它" refers to "shop". But you need to cut the end that "了". so the full sentence could be: 这家商店很好的。它的衣服不太贵。

@Yvonne's answer is right. But we always use @Tinashi's answer, it seems more natural.