There are actually two questions in this post, which I'll address separately.
The first question is "Does the thrust from multiple engines add together?" And the answer to that is yes, so long as both engines are mounted so that their thrust vectors are parallel, two engines, each producing 6 kN of thrust, will produce a total of 12 kN.
The second question is "Can I just bolt a second engine onto my airplane to make it go supersonic?" There's not enough information here to accurately answer that question, so the closest I can get is "probably not".
The maximum thrust of the engine doesn't matter. What matters is the actual amount of thrust produced by the engine in the conditions you expect. You mention the maximum thrust is achieved at sea level. But you're not likely to be flying at sea level, are you? You're going to be flying much higher, where the air is thinner and therefore wind resistance is much less, but you're not going to get the full 6 kN at those altitudes. An engine designed for subsonic speeds also isn't going to produce its maximum rated thrust at transonic or higher speeds, so you're also going to lose thrust as your speed increases.
There are other factors too. There are all sorts of interesting shock waves that form in the transonic region, which could either starve your engines of air, force too much air into them, or even damage the turbines. Adding baffles as you mention is going to add a lot of drag, which will need more thrust to counter. Another consideration is that the simple weight of the engine will require more thrust to lift. So even if your "9 kN" calculation is accurate for the plane as-is, it's not going to be accurate after you've made all these modifications to it.
Another thing to consider is the strength of the airframe. If you put a second engine on a frame not designed for it, you're going to damage and probably destroy it.