The fact that you can hide an entire combat fleet consisting of multiple capital ships in an asteroid field or dust belt tells me that technology to hide a ship's heat signature is exceptionally advanced, at least from long range, but I also suspect short range as well, i.e. combat distances. Flares are also fairly common on more civilian-type ships, and can have high success rates in either causing a missile to explode prematurely or fooling it into chasing one. One can also assume there's other procedures that follow dropping flares, for example modulating engine output so it more closely matches the flare signature, etc.
There's also the thought that missiles use a form of guidance we're not familiar with today. Many Domain-era weapon, for example the Heavy Burst Laser, mention that no one really understands how they work, knowledge lost since the Collapse. I won't think it would be too much of a stretch to say that either the missile guidance tech is commonly understood, but not explained, or that it might not be understood well enough to go into depth about it.