There are two possible (although very much related) meanings of configuration here.
If you take "configuration" to mean "the act of configuring", only "shop configuration" is grammatical (compare "airplane flying" and "ship navigation").
If you take "configuration" to mean "the result of the act of configuring", then you could use either "shop's configuration" or "shop configuration" (or maybe even "shops' configuration" if you can have one configuration associated with multiple shops).
I would guess that you want to allow for both meanings (because I am assuming that your website lets the users configure the shops), so I would suggest "shop configuration".