Penguin Readers is a series of books organized, and in some cases edited, to provide interesting reading at different levels to people who are learning English. They have seven levels, which range in difficulty from "Easystarts" with 200 headwords (that is, main words with variations) through Level 6 (Advanced) with 3,000. The catalog you provided as a link is from the next-to-the-top level, with 2,300 headwords.
To use your example, "shop" would be a headword. It might be used as "shop," "shops," "shopping," "shopper," "shopped" or in other forms. It's still one headword.
I don't know if that figure applies to each book in the series or to the total of the entire series. Probably each book, though. A different book might have different headwords, but about the same number of them.
This is not common usage. The catalog is probably intended for teachers who will choose reading materials for their students. It's one measure of how hard the books will be for students to read.