Duncan,
I wouldn't use an Ikelite dual cable and the black storage cap as a single strobe conection 
I know one person (very experienced photographer) who says he does it all the time using the BLUE banded cord on a single connection. But as an Ikelite dealer AND user with years of experience my information says the black storage cap is simply an o-ring protector. The internal diameter is barely larger than the o-ring's outer diameter so it does not put any excessive pressure during long term storage. I believe it eve says on Ikelite's web site this is NOT waterproof for diving.
So to me this is just asking for a flood up the capped dual cord end.
Most Ikelite dual strobe shooters (me included) have TWO dual cords and one SINGLE for a back up on trips. As I've also said before I don't understand all these cord failures.....I get to dive a bit more than many folks (I see people posting 50-100 dives / year) and they seem to be breaking these things like hotcakes........I certainly don't wrap mine around the strobe arms like an Anaconda, but I don't baby them either.
As far as linking an EV controller inline as an emergency measure YES, you need to totally cover the EV controller with the black cover or it will trip each time it "sees" another strobe fire. Plus you need to set the strobe head on TTL as you are now MANUALLY OVERRIDING the strobe with the manual choices on the EV controller. In essence, no TTL.
Hope this helps.......
dhaas