Internally in C/C++ n dimensional arrays are identical to 1 dimensional arrays. They don't involve pointers, but are a single region of contiguous memory such that an n-dimensional array can always be indexed as a 1 dimensional array. So, n dimensional arrays consume the exact same memory as 1 dimensional arrays. The standard way C indexes arrays is y*width+x which is not slow or unreadable, but is and has been the standard way that multidimensional arrays are accessed at the low level. C has always translated map[ x][y] into map[y*w+x].
Again, there is no performance hit for this, it is the standard way that multidimensional arrays have always been accessed. If you are really crazy about performance, you can still loop over a multidimensional array with a pointer increasing the pointer with ++ for every entry to prevent the multiplication, but you'll never notice a performance increase. Multiplication is a crazy fast operation.
In terms of [ x][y] versus [y][ x], it won't affect performance on modern machines either way, but tty based displays drew the screen from left to right top to bottom making [ x][y] make more sense. I think virtually everyone uses [ x][y], and every open source program I've seen uses [ x][y]. I use [ x][y] too. As Jo said, [ x][y] is the standard in math, physics, and most importantly programming.