I have had a multitude of different crystals ranging from flat sapphire crystals right through to a Rolex superdome plexi crystal and in all honesty I haven't noticed any difference in the risk of damage.
Personally I prefer acrylic or hesilite crystals with a dome. They are more tactile and easy to sort out in the event of an accidental scratch. I appreciate that the overwhelming number on here prefer the scratch resistant sapphire type crystals, but if you do damage them, edge chips etc repair is almost impossible unless you are extremely skilled.
And finally, I just prefer the look of a domed crystal.