No,
once set you should never need to change the soft limits unless you physically move your hard limit switches.
Yes, if you fit a longer tool after a shorter tool, it WILL crash IF you tell it to go too low - this is life in the world of CNC - YOU are in command of the code that tells the machine what to do.
IF that code is written properly AND your machine is setup correctly for the job in hand, the tool will NOT crash the table
You need to know exactly what your code is going to do with whatever tool is fitted BEFORE pressing the start button or things will get expensive very quickly - we have all been there, i busted probably £100 worth of end mills in my first week after i built my milling machine, now it rarely happens, just chalk it up to learning.
There are very few safety nets in CNC - the machines are dumb servants and merely follow your command - you must be in control.
Having said that, it's a blast when it all works - what a ride