If you're talking about hitting them in the air with it, it's totally dependent on their position in the air, or, if you're doing it in mid-combo, on the amount of proration (hitstun?) your combo has the moment you decide to go for the chains.
If you think you've hit them too many times before the launcher, just stick to 1 hit. Don't get greedy. :V
If you're talking about ground chains, you can only hit them with a second chain if the first hit was a counterhit.