Thanks for catching these bugs! I've confirmed you're correct that the EMP missile 2 is bugged, I'll have it fixed in the next update. I have tested the repair bay before and seen it working, but I'll give it another pass. In looking at the code I do see a potential issue that could cause it to not trigger on modules that have had their hp increased with upgrades or crew.
For the chain reactor, yes it will give the evade point if the last action that played before it was another chain module. So if you put two chain modules in a row (either the same module or other "chain x" modules), the second one will get its "chain: ..." ability, but not the first.