Data Science in C (or C++)
Or must I loose most of the efficiency gained by programming in C by calling on R scripts or other languages?


Do the opposite: learn C/C++ to write R extensions. Use C/C++ only for the performance critical sections of your new algorithms, use R to build your analysis, import data, make plots etc.

If you want to go beyond R, I'd recommend learning python. There are many libraries available such as scikit-learn for machine learning algorithms or PyBrain for building Neural Networks etc. (and use pylab/matplotlib for plotting and iPython notebooks to develop your analyses). Again, C/C++ is useful to implement time critical algorithms as python extensions.