Because it's a bug, not a feature. 
Joking aside, I'm sure that moders might like the option to make that kind of a decision themselves.
"Pilots, we just got this new weapon in. Its not as good as the missiles you've been using lately, but thanks to an improvement in the on-board targeting sensors and IFF, it can track an enemy fighter even if your fighter's scanners can't. You'll find it most useful against fighters from the RealyBadAliens, who often employ stealth technologies to reduce their ship's power signatures below the targeting threshold of your scanners."
In ai_profiles.tbl:
$heat-seeking missiles track invisible ships: yes/no
$heat-seeking missiles track stealthy ships: yes/no
(and just for more possibilities)
$aspect-seeking missiles track invisible ships: yes/no
$aspect-seeking missiles track stealthy ships: yes/no
and/or in weapons.tbl
$track invisible ships: Yes/no
+(the same set of figures as follows $Homing, so the moder can specify if this missile's tracking ability is worse when attempting to track an invisible target as compared to a normal one)
$track stealthy ships: Yes/no
+(ditto)
The extra homing data would be optional, defaulting to the same tracking figures as under the normal homing section. The moder may add view cone to aspect seeker missiles, where no view cone is specified under the main homing data, since it has to be able to seek its target when none may be designated.
