You are asking a complicated question, I will try to explain the various issues involved and then the Halacha l'maaseh.
The coffee beans themselves grow on a tree so they should be ha'etz, except that they are not really edible alone. However the Mishna Berura concludes that something bitter that only becomes edible when candied retains its beracha of ha'etz.
Chocolate is also derived from the fruit of a tree, and despite the change in appearance from its natural state should retain its beracha of ha'etz since most cocoa beans are made into chocolate. However the prevalent custom is to say shehakol on chocolate, and the Poskim give numerous explanations for the custom.
When two food items are combined the beracha on the resulting item follows the primary component. The Mishna Berura writes that with a coated nut the nut is always the more important ingredient regardless of which is the majority, but most Poskim including Reb Moshe Feinstein zatzal disagree. In your question you describe the chocolate as being a thin layer, but on the other hand it is difficult to say the inedible bean is the more significant part. I think most people would consider the food to be chocolate with a coffee bean added for flavor and texture, rather than primarily a bean with some chocolate to take off the bitterness.
In conclusion, the ideal solution would be to take two other foods, one that is certainly ha'etz and one that is clearly shehakol and make the berachos on them before eating the chocolate covered coffee beans. If this is not practical, the better choice would be to say only shehakol, as this is the customary beracha on the primary component. However the argument could be made that the coffee bean is certainly ha'etz and even the chocolate may be as well, and therefore ha'etz is also acceptable though not preferred. In any event, in this situation one is yotzei b'dieved with either of the two berachos.