A stealth ship tries to minimise it's emissions and reflection on whatever band on the spectrum the enemy tries to use.
BTW those eye comments: do you know how freaking advanced thing your brain is? Just because you see smg. doesn't mean you'll notice it. Your brain can interpret that image and realise it's a ship's trail you're seeing - a computer may have trouble doing so.
Space is huge - you can't even find a goddamn planet if you don't know where to look. In spaceoperas it seems quite simple while in real life™ it would take days of observations to calculate a single planet's position.
If subspace interacts with gravity - and we're inclined to thik so- than it becomes a bit easier, but it's still a complex task.
Now imagine how hard it is to spot a single warship smaller than a bigger asteroid?
The only thing I can think of is to listen for distinctive radio/EMwave signals the ship might emmit from its engine or reactor - if both are powered down you're in trouble. Of course the hiding will run low on battery power eventuelly.
You may look for the actual gravity of the craft but that method only works in deep space, and the presence of any planet can screw things up, since you're looking for extremely minute changes caused by a ship with neligable mass in terms of gravity.
(Asimov uses this method in his Empire books - Currents of Space e. a.)
FS radar is probably some advanced radar that scans for engine signatures - since you use fusion engines you inevitably create a lot of waste signals on the spectrum - nuclear reactions tend to do that.
At this point it becomes smg. similar to today submarine warfare - you can even identify a single vessel by it's distinctive sound if you have a previous sample.
So a stealth craft doesn't have to be all that stealthy to begin with - especially in a nebulae.
Of course big active radars can pick you up - this is the reason big ships send you the target data most of the time.
However just like active radars today using one equals shooting at the top of your lungs: "Hey, I'm here buggers!!!"
Of course it has it's own troubles - in a stellar system it takes EMwaves minutes and hours to get to a planet, and it takes a huge ammount of energy to cover an area that big a have an echo.
So EMwaves are good for only short range scans only.
Therefore I think any long range scan requires subspace radar or an equivalent.
If detecting something is this hard when designing a stealth fighter all you have to minimise is EMWave stealthyness - just as with a craft built today. This includes the heat signature.
That's about detecting something.
Locking on is an entierly different thing!
You have to know the precise position and speed of the craft - and let the missile know it too.
In FS they don't use radar guided missiles - maybe since fighters only have passive radars - only optical (aspect seeking) and heat seeking remote weapons.
However there's no such thing an invisible craft!!
Even a stealth fighter/bomber will have a radar/EMwave signature as well as heat signature.
Therefore some weapons will still be effective against such craft at very short range.
Heat Seekers definitly - aspectseekers may have trouble since they are optical guided and even if they mange to lock on to the stealth craft it's very vague shape and unusually low profile can screw them.
You could build special rockets to be used against stealth craft, but these sensors will have to be so sensible that ordinary signatures may burn them out.
With heat you don't have this problem - even the best insulated craft will have a heat signature - although an IR aspect seeker could use that too, let's assume that FS ships emmit heat only with their engines - and give a heat seeker a chance to get it.
