I tested a spaced armor design that actually absorbed a lot of damage from a 10-block long d1000
The design had a one block think plate 8 blocks away from another one block thick plate that is supposed to be the hull. The missile detonated on the first plate. The missile blew a hole in the first plate but only managed to damage some blocks on the hull, but none were destroyed.
I would suggest this as a cheap and effective defense against heatseekers.
EDIT: Whats a good 5x5x5 reactor design?