Thank you for your question. I apologize for the delay in answering.
Yes, there will be an upgrade fee for each additional storefront. It will be lower than the price of a CS-Cart Professional one-year upgrade subscription plan, so it will be much cheaper to upgrade a Multi-Store installation with 5 storefronts then 5 separate CS-Cart Professional installations.Will each store license after the initial 3 storefronts have to be renewed "Prolongate" each year or will there be a single renewal "Prolongate" option for the primary Multi-Store license? Considering that an additional license has to be purchased for each store after the initial 3 storefronts, if a yearly renewal "Prolongate" is required for each store, then the attractiveness of Multi-Store is seriously waning.
Also, in case of a Multi-Store installation, if you have some changes in the PHP source code and they conflict with an upgrade, it will be required to resolve them only once for all storefronts, because (I would like to remind this fact) all the storefronts are served by a single software installation.
Thus, if you have several online stores, it is reasonable to use CS-Cart Multi-Store Edition for that, because it is
1) more convenient;
2) time-saving;
3) cheaper.
Lastly, I would like to note, that an upgrade subscription plan is not something mandatory. A CS-Cart license gives you the right to use a purchased version of CS-Cart for an unlimited amount of time with no additional fees. But if you want to add some new cool add-ons to your store that we include in CS-Cart releases regularly, then yes, renew your upgrade subscription and beat your competitors finally!