From Ryan of UWCP in regard to the black-caps, and confirmed by Ike of Ikelite:
"Unfortunately, the Dual Sync Cable's caps are not waterproof, so you'll need a single cord for use with the single strobe, and need to purchase a dual cord when the second strobe is added."
Reason:
"The caps are merely dust covers to keep the o-rings clean, and do not exert any pressure so o-rings are not deformed in storage. There used to be all kinds of crazy recomendations with Nikonos cameras about storage o-rings, etc, so Ike just made caps that didn't affect the sealing surface."
~Matt Segal