NASA actually did studies that say that it does increase the thrust. Air moves faster on top of the wing than the bottom, so could this have an effect on the engine's performance if there is more intake of air into the engine if the engine was mounted on top of the wing instead of the bottom?
First, we need to agree what thrust is. The simplest definition would be to measure the pressure in the intake and the nozzle, as described in the answers to this question.
But this gets you only so far. It would be more complete to use the difference in horizontal forces acting on the plane between idle and full thrust for the definition, because that is really what interests the pilot. Imagine that your engine will cause massive separation around the intake at idle (spill drag), or that the exhaust jet will help the flow over the deflected flaps to stay attached, avoiding the drag of separated flow.
If we can agree to include the change in drag into our thrust measurement, the next question is what flight segment is used? In cruise, the flow around wings and fuselage is nearly completely attached, and the engine can only spoil the orderly flow. Next, since the speed of flow is higher on the upper side of the wing and the intake needs to decelerate the flow, a top-mounted engine would need to decelerate its intake flow more than one below the wing. This leads to higher intake losses and less net thrust. Conversely, if the engine is below the wing, the wing will already decelerate the flow somewhat before it is ingested by the intake, which makes the work of the intake easier and reduces losses.
In the landing configuration, however, a deflected flap blown by the engine exhaust will create a much better L/D than one without. In this case, it is better placed on top of the wing. The Boeing YC-14 and the Antonov 72 are examples of such configurations.
Since the cruise segment is much longer, most designs prefer to place the engines below the wing, but quite a bit ahead of the aerodynamically ideal position to shift the center of gravity of the wing ahead of its axis of elasticity, thereby helping to dampen flutter.