Does other insurance pay for damage to car mods?

im pretty sure my car is totaled, a drunk driver t-boned my car after running a red light and the damage is really bad. im positive that insurance will decide in my favor and send me a check for the damages, but do they take mods i did to it in account? i had a k20/k24 frankenstein motor swapped into my car. i also had a nitrous line going into the motor. its a 2003 honda civic EX which normally i wouldnt get much for but i invested a shitload of labor and money to make it the way it was