No it shouldn't. Every system has a soft reset code, and they're not designed to damage the system.
Also, if you soft reset while it's saving, it's still unlikely it'll damage the system, more probable it'll just potentially corrupt the save file and revert to the backup later Pokemon games store on the game card.
It does not damage the system while saving. Think about what happens when you save, you are modifying the game save file and that is it. You aren't modifying any system files on the 3DS you are just using system functions to process the save. If you restart while using a system function it won't corrupt that function because nothing is being written to that function. You'll still be able to call it again and again.
The reason why you get corrupt saves is that the save file doesn't get fully written.