I haven't had any issues with saving the ships yet - though the game has crashed once when I tried to copy and paste a massive slab of armor (about 102x102 size) but that's probably due to the size of the part.
I tried saving the game once, and although it was slow - it didn't crash.
The issues I did notice were that white artifacts on the ships when I zoomed out and the green damage indicator model on the bottom left looked weird. I've uploaded the ship I was playing with here:
