If you mean soft resetting to get the Shaymin or Darkrai you want, than yes it is completely safe. There is nothing dangerous about Soft Resetting; which is the reason they added that into the system. It is there for the reason so that you don't have to "hard reset" your hardware over and over again (turning on and off unexpectedly).
The only danger is making sure you saved the game beforehand if you wanted to.
- EDIT: If you were talking about Tweaking by using the Surf Glitch to get to the islands to capture Shaymin and Darkrai, than yes it is still safe to stay there and Soft reset in those areas.
Because you catch Shaymin at Flower Paradise and Darkrai at Newmoon Island, which are real areas in the game, its totally normal to walk around and save in those maps.
The only danger in tweaking is by travelling in the "voids" of the game (or black areas of the game), once to get to those islands or a NORMAL game map, you are totally safe.
*Please note that I have never tweaked before in my life or ever used this glitch, so there is a possibility I might of missed a piece or information or be wrong somewhere.
