Unfortunately this problem runs very deep. When you stack extremely powerful Omega techs onto an already extremely powerful Stellar Systemcraft, you end up causing an integer overflow on either the armor/shields which causes them to loop back around to 0. Stellaris uses 32-bit integers to describe values such as hull, armor, and shield strength, which means that their values cannot exceed 2^32 = 4.3 billion.

The only way to fix this problem would be to go into Stellaris' Clausewitz engine and recompile it to work with "long" 64-bit integers instead, which would likely cause some really fundamentally game-breaking bugs. The alternative would be to avoid using such overpowered techs on the Stellar Systemcraft in the first place; I've successfully managed to get it to run with most of its components running Phi tech instead.

my way of bypassing the issue was to construct a total of 5 systemcrafts and outfit them all with stellarite components