This change to the Portfile got it to build for me; apparently those files are in a different location now, so the original pre-check failed (properly installed Xcode and command line tools will find it regardless of the pre-check, so this is all that needed to be changed). Since soprano is a prerequisite for kdelibs4 (and therefore all that depends on, like kdegames4!!), this was really a problem for me until I found the workaround.
bigapple:soprano root# diff Portfile.orig Portfile 45c45 < if {![file isfile "/System/Library/Frameworks/JavaVM.framework/Headers/jni.h"]} { --- > if {![file isfile > "/System/Library/Frameworks/JavaVM.framework/Headers/jni.h"] && ![file isfile > "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/System/Library/Frameworks/JavaVM.framework/Versions/A/Headers/jni.h"]} > {