The merchandising side of the club had been loss making for years. Way back when Johnson took over he was shocked to find the club was so far behind the times it only had about a 50k merchandising budget and nowhere proper to sell it, hence him building the Everton store (unfortunately while Johnson was building a corner shop, United and Newcastle were building massive stadiums and breaking international markets). The current board tried to take it further by opening a store in the city centre but the demand simply wasn't there so it was making big losses. They then made the disastrous decision to combat this with a deal with JJB to handle the retail.
They turned to Kitbag (who do the merchandising for Real Madrid, United and Chelsea amongst others) to take over merchandising, in a deal based on a fixed amount paid to Everton plus some extra based on sales. With the previous shop making such losses in the city centre, Kitbag wanted to make sure they were the only place you could get Everton merchandise so the shop would make a profit, so they made the two stores and online the only place you could get official merchandise.
So basically the club has a choice, either have a city centre store, or have merchandise that can be bought anywhere, because past evidence shows we probably don't have the demand to be able to keep both going whilst making a profit.