It depends on whether or not you want the savegames to maintain binary compatibility with the original savegames. If not, it doesn't matter if the system is big endian, since the data would be read back in the same byte alignment format as it was written in.
Of course, endian issues do matter when reading in the game datafiles, which is why ScummVM, for instances, has macros like READ_LE_UINT16 and FROM_LE_16 to read values in and swap the bytes if compiled on a big endian system.