I'm almost positive about this, but it probably can't hurt to check: if I use an LRM launcher loaded with swarm munitions (p. 371) to make a called shot (pp. 78/79), any secondary attacks that result (a) do not count as called shots themselves and (b) as a consequence do not incur the +3 to-hit penalty for one.
Right/wrong/partially right/somehow completely messed up? :)