I have several webshops. Do I have to make a separate application for Kassa Compleet for each webshop?

You only need one contract and application to organise the payment traffic to several webshops.
You can use one Kassa Compleet subscription with one IBAN accounting number per PLC (registered with the Chamber of Commerce) with several webshops.
For this, you pay a one-time subscription fee. You submit which payment methods per webshop you would like to provide.