Trav missiles are FAR too small to incorporate sub-munitions that are large enough, or powerful enough to damage a spaceship hull.
Aside, of course, from the Multi-Warhead Missile.
There is no ECM for the hot missile.
Without really thinking, three comments:
1) IR baffling to reduce the heat signature of the missile - you can't eliminate it but you can radiate as much as possible back towards the launching ship not the target. In addition, (pulling out Universal Traveller answer No. 3) It's A Feature Of Gravetic Technology - if a missile is using a grav system for acceleration then it needn't necessarily have a hot exhaust plume (which is what IR systems generally see rather than the missile itself).
2) Flare ejectors dispensing short-burn decoys on similar vectors.
3) Relatively low power, low-coherency (i.e. wide 'spot' angle) IR-frequency lasers which strobe back and forth over the target. Any time the laser sweeps over one of the ship's IR sensors, it will be temporarily blinded because the entire field of view will be saturated. Now multiply by one or two of these devices in the nose of each of a barrage of 100+ missiles....
Large Aircraft Infrared Countermeasures is a current equivalent of this technology.
http://www.globalsecurity.org/military/systems/aircraft/systems/laircm.htm
For example, several of the latest designs of anti-ship missiles
are much more like torpedoes, they submerge a long distance from the
enemy ship and then attack submerged, exploding under the ship
Interesting. I know ASROC, Ikara, etc, deliver torpedos, but they are short ranged (~20Km) anti-sub, not ship-to-ship weapons with the 70+ km stand-off range needed for that sort of fight. Which missiles did you have in mind?