Next update will see a change to how missiles work.
This is the best image I have at the moment to detail it:
The target is made of a 10m thick plate of grey advanced armor, behind it was a block of power reactors.
In the upper right you can see two small holes, both made by my 10mil damage/missile missile/pulse combo. The missiles penetrated 3 blocks into the armor, but the armor HP pool absorbed 50% of the damage.
In the upper left, is the first shot that cracked the armor HP pool. It still didn't penetrate the armor itself.
The bottom left corner shows a shot that hit the armor without a hitpoint pool to absorb damage. Any system blocks behind it would be drilled through at the diameter of the hole in the last layer of armor penetrated as shown here:
(This is using a different target, with 10m thick armor, 10m of power capacitors, 10m of thrusters, then 10m of power reactors)
The entry wound
Exit wound
The central hole is what it looks like after a second round has penetrated, destroying a ~100m diameter section of systems blocks, and some armor on the inside.
All the little holes are from a cannon/pulse combo I was testing simultaneously. It penetrates advanced armor, and systems, extremely effectively as well, with only 2k blocks in both cannon and pulse separately.
Here's a shot that wen through the plate (second target) widthwise, for maximum length:
Upper shot penetrated without armor HP pool, lower with it. It doesn't make a whole lot of difference in this case, because the cannon had enough damage behind it to bore to its maximum extent either way.
So the nuke will still nuke, if it hits system blocks. However, you CAN armor your craft to withstand a serious multi-million-damage assault, if you have a high armor HP pool and take advantage of actual, serious capital ship armor plates on key points or multiple-meter thick armor all-around.
It's also important to note my missile system was only a few thousand blocks in total size, but relied on a still larger power capacitor. The cannon totaled 4k blocks. no effects were used in either, and targets were unshielded.