After many experiments I found partially working solution with FreeImage_ConvertFromRawBitsEx
:
FIBITMAP* bmp = FreeImage_ConvertFromRawBitsEx(true, buffer, FIT_UINT16, 1000, 1506, 2000, 16, 0xFFFF, 0xFFFF, 0xFFFF);
(thanks @1201ProgramAlarm for hint with masks).
In this way, FreeImage loads the data, but in some semi-custom format. Most of conversion and saving functions (tried: JPG, PNG, BMP, TIF) fail.
As I can't load data in native 16bit format, I preferred to convert it into 8bit grayscale
unsigned short* buffer = new unsigned short[1000 * 1506];
// load data
unsigned char* buffer2 = new unsigned char[1000 * 1506];
for (int i = 0; i < 1000 * 1506; i++)
buffer2[i] = (unsigned char)(buffer[i] / 256.f);
FIBITMAP* bmp = FreeImage_ConvertFromRawBits(buffer2, 1000, 1506, 1000, 8, 0xFF, 0xFF, 0xFF, true);
This is really not the best solution, I even don't want to mark it as right answer (will wait for something better). But after this the format will be convenient for FreeImage and it could save/convert data to whatever.