Your son is in luck. If he's going to lag behind in one subject, then he picked the “right" one. Many college officials … even at the hyper-competitive colleges … have observed that foreign language classes can be an Achilles Heel. Some high schools (especially public ones) don't have great language programs, and thus otherwise strong students don't fare as well in these classes as they do in their others. Sometimes, too, the classes are fine but the student–for whatever reason–just doesn't “get" foreign language.
If your son's grades and tests scores are strong in math and sciences, then admission folks at RPI, WPI and Case Western Reserve should not penalize him for his downfall in Spanish. Case, by the way, is one of those great “sleeper" schools that isn't insanely hard to get into and yet has an excellent reputation. The students are smart too. In fact, Case probably gets its share of those who aimed for Stanford or MIT but didn't quite make the grade … perhaps in Spanish. 😉
So don't worry. If all else looks good, the Spanish grades won't hurt. And maybe down the road, your son will learn Spanish the way it's supposed to be learned … by living in a country where it is spoken. WPI, for instance, is big on global projects and there are several in Spanish-speaking countries. See http://www.wpi.edu/academics/igsd/project-centers.html So perhaps your son will end up in one of them and finally learn to speak Spanish after all.