That specific "bug" is really the way whmcs operates. If a client enters card data before placing an order, there is no payment gateway associated with them(technically the order, but for the sake of this, we'll say the client), and it will then store the details locally, based on how WHMCS is configured. Most clients are not going to do this, instead they will supply card details as part of an order, and decide then whether they want to store their details with you or not. Again, this is independent of any gateway.
In terms of zStripe, when the card details are supplied during order, or anytime after that, the card data is taken via your site, hopefully over SSL and transmitted the Stripe. No data is stored locally unless you have the option to store locally in the gateway configuration.