Set in a quite distant future, intergalactic war is brewing and it is important to tell what form of attacks the enemy ship is using otherwise the battle will quickly become one sided. Anyway imagine a torpedo in the form of a kugelblitz is being deployed in battle, the micro blackhole is then accelerated to close to speed of light so that the spaces between itself and target becomes small granting it enough time to evaporate into deadly Gamma. But from the enemy frame of reference how can they tell? What technology and methods can be used to establish the nature of the attack?
An object between an observer and a light source will affect light coming from the source.
In simpler terms, a kugelblitz is a black hole formed from radiation as opposed to matter. (Such a black hole would nonetheless have properties identical to one of equivalent mass and angular momentum formed in a more conventional way, in accordance with the no-hair theorem.)
The no-hair theorem states that all black hole solutions of the Einstein–Maxwell equations of gravitation and electromagnetism in general relativity can be completely characterized by only three externally observable classical parameters: mass, electric charge, and angular momentum.
A Kugelblitz is coming fast. Light is faster.
The Kugelblitz will be a darkened area against stars behinds it. This is true also for an incoming meteor.
Unlike the meteor, the Kugelblitz will intercept radiation from an area greater than its profile because its gravity will bend in and capture photons that otherwise would pass near it and on to the observe. It might appear as a meteor larger in diameter than the Kugelblitz is.
The Kugelblitz (by virtue of its gravity) will bend light near it that it does not intercept. The relative positions of stars on the far side of the incoming Kugelblitz will appear to change. This is actually true for normal masses also but by a trivial amount.
These effects would be noticed immediately by a computer whose job it was to watch the stars in all directions. If a fixed distant star blinks out or appears to move, something is in between you and the star. Observation over a period of a second will allow the trajectory of the incoming object to be calculated.
You will move out of the way and wonder how much it cost to throw that very expensive rock.
A micro-sized black hole will be a powerful source of intense gamma rays and interesting particle radiation; that's just the nature of Hawking radiation. A hole which evaporates in a second is emitting zettawatts of EM and particle radiation. A shorter-lived hole will be proportionally brighter, and even if it were travelling at highly relativistic speeds the journey will not be instantaneous and radiation will be emitted and so can be observed.
Because of the sheer speed of the emitter, observers who are watching it fly towards them will see the radiation strongly blueshifted, and observers watching it fly away from them will see it strongly redshifted. This will make it obvious to everyone involved that the projectile was a highly radiant relativistic object. The spectrum and types of emitted radiation will show that it is not merely an extremely hot blackbody, but clearly something that's pulling a wide variety of particles out of the quantum vacuum. To me, at least, this seems trongly suggestive of a black hole, but perhaps there are other phenomena that could do this too.
It will not be possible to distinguish a kugelblitz from any other kind of black hole, due to the no-hair theorem mentioned by Willk.
As a footnote though, consider that if you can accelerate non-trivial masses to high relativistic speeds, there's absolutely no reason to fire anything other than boring, regular matter. The kinetic energy of the projectile is such that the contribution of its mass-energy to the total amount of boom becomes increasingly uninteresting. This is why there's no point making an antimatter particle beam, for instance.
The amount of energy released by a black hole in its final moments cannot exceed the mass energy of the hole. At speed of .9c, more than half of the energy released at the end is the kinetic energy of the projectile. AT .99c, the kinetic energy is more than 22x the mass energy.
You haven't specified how fast your "torpedo" is travelling, but there's a reasonable chance that you've simply made things much more complex and awkward than they need to be. Take the energy you would have thrown into the kugelblitz, and use it to shoot a bigger or faster projectile, or make several shots. Saves carrying all those dumb, heavy, power-hungry, massively hot gamma ray lasers nailed to a fiddly and probably delicate mount, too.
The sensor blitz.
The other answers are pretty good, but just for fun variety, when a ship arrives in a destination that they think is dangerous and might get attacked, they could launch cluster bombs that each contain thousands of micro-sensors, the size of a penny or whatever. They fill the entire surrounding space for thousands of miles with these, which signal the ship when they detect a kugelblitz heading in. Either by radio, which is still faster but don't give a huge heads up, or by quantum entangled communications, which would be instantaneous (if not entirely in keeping with our current understanding of physics).