[Spinnaker]

If there wasn't a good reason for putting them there, they wouldn't have put them there in the first place. No company is going to go to the expense of engineering and designing a part, manufacturing the part, adding the part to the assembly process, and then expending the labor to install that part, if it isn't needed. Everything costs money, and if they can eliminate something, they would have to save the cost. It is the economics of manufacturing, keep the cost down to maximize profits.
My guess would be that it directs cooling air into an area that needs it. There is not a lot of air circulation in the engine area, since it is a mid engine design and the radiators are in the front. Unlike a front engine car that gets cool air rammed directly into it at all times. The exhaust manifolds and catalytic converters are in this area and are high temperature emitters. The engine compartment is very crowded in the Boxster and everything will get hot back there. The rubber spoiler scoops may help keep the temperatures in this area manageable. Higher temperatures generally mean lower component life, whether it is mechanical or electrical in nature. There may be a safety issue, elevated temperatures can be a fire hazard. Ever notice how hot the trunk is after a long drive? If I pickup a pizza to take home, I always put it back there it keep it hot. I remember reading a forum post about someone putting their shoes back there and the rubber melted.
Some of you engineers can chime in if my guess is off base.