Microsoft's own versions of these functions, CString, and std::string, are less likely to cause security problems. (I haven't had problems with strlen, but strcat and the other functions require some diligence to use properly.) If the warnings are problem to you, you should find a compiler switch that turns off the warnings.
It seems I've misread or misinterpreted something when on this thread I read through the link posted that microsoft deprecated most of the C library. For instance, functions like strlen() have been deprecated by Microsoft owned library in VC++ 2005 and added their own versions of these functions. strnlen() on this case.