< We will be arriving late (around 9pm) at the Bruges train station >
9 p.m. is not late at this time of year. I am typing this in Brussels at 9 p.m. and the sun is still shining !
< Should we take a taxi Or is it walking distance? >
I would say it is too far to walk and you should take a taxi.
< Is it safe to walk at that time of the night? >
Of course - but your apartment is quite a long way from the station and may be difficult to find in a complex street pattern http://goo.gl/maps/GB4n
Station is in bottom left-hand corner. "A" marks Sint-Jansplein 5. Even in a straight line on the map it is more than 1 km - and of course the streets don't allow you to walk in a straight line.
< Is it easy to find a taxi at 9pm outside the station? >
Probably - someone actually in Bruges may be able to give better advice.