Thank you for your question. I have seen different coaches prefer the second baseman and others the shortstop. And sometimes it switches whether there is a lefty or righty at the plate.
That being said, my preference is to have the shortstop cover because:
1. The shortstop is in a natural position to catch and apply the tag. The second baseman at some point in either her route to the ball or when catching the ball, must turn to apply the tag.
2. The shortstop is usually your best athlete and best fielder. I want her trying to flag down poor throws or wild bounces.
3. The shortstop can use the bag to protect herself at some level.
4. You actually want the tag placed out in front of the bag, so it is obvious to the umpire that the runner is out.
Ok, so that is my view. I have no doubt that those who advocate that the second baseman cover will have equally valid reasons. Please join in.