tl;dr: The idea of a sub-atomic black hole as a warhead is great, but how are you going to hit anything? If you have 1e23 Joules to play with, a directed energy weapon or railgun is much more effective and requires no unobtanium machine.
That black hole doesn't come for free, nor does firing it at any appreciable speed. As much energy had to go into creating it as it is capable of releasing. Probably A LOT more. The question becomes...
What else can you do with 1e23 Joules... IN SPAAAACE!!!
and
Why aren't you doing them? In space.
As with every weapon system we must ask whether it's a significant improvement over the alternatives? This is difficult to answer without knowing the state of offense and defense, and the presence of one unobtanium machine throws all physical limits into question, but there's still one problem.
Hitting Things (in space)
It's really, really, really hard to hit things in space, especially if they don't want to be hit. Sci-fi depicts spaceships lobbing broadsides into each other at point blank range. In reality, everything in space is so far apart, and traveling so fast, that your ability to track and predict the movement of your target becomes paramount.
Speed of your projectile is also paramount. Just like on the ground, the faster your projectile is going, the less time it has in flight, the easier it is to aim, and the less chance the enemy will maneuver away. At a certain point increasing your range is pointless; the flight time is so long that the enemy can simply turn in any direction to avoid your shot. For battleships this was about 30 seconds. Any more distant and the enemy captain simply had to turn when they saw the flash of your guns.
But space has a speed limit, the speed of light. This introduces two very interesting problems. First, there is a maximum effective range in space for unguided weapons, and it's A LOT shorter than you might think. Let's say your ships have a roughly 100m cross-section. The target only has to maneuver 100m in an unexpected direction for an unguided payload to miss.
At the energy levels you're playing with a ship's delta-v is limited only by how much stress it can put on its structure and its crew. Let's say it's 9g's, the limit of human endurance.
How long does it take for a ship able to accelerate at 9g's to move 100 meters? 1 g is roughly $10\frac{m}{s^2}$. 9g is roughly $90\frac{m}{s^2}$. So a bit over a second.
In one second, a ship can maneuver out of the way of an unguided projectile. This means even an energy beam has an effective range against a maneuvering target of 1 light-second or about 300,000 km.
The second problem is, unlike a battleship, light delay means you're seeing where they were 1 second ago further complicating the aiming process. OTOH if the enemy sees "the flash of your guns" they've been hit. However, the target only need to make random zig-zags during combat to remain effectively immune to unguided weapons beyond 1 light-second.
Directed Energy (Space) Weapons
If a sub-atomic black hole can penetrate their defenses, then a focused, high-energy photon beam can as well. It's even smaller, and it also has no electric charge. It travels at the speed of light making aiming as easy as it's going to get. What's not to like?
Range. As the range increases, the focus will decrease. This puts a limit on the effective range of an energy weapon; eventually it's so defocused that it's no longer effective. But effective unguided range is already limited to 1 light-second, so this isn't a big problem. And that defocusing might be a good thing, the weapon can hit a wider area.
A Well-Aimed Space Rock
If you're going to fire this black hole at a ship unguided it has to be going as fast as possible. Let's say 0.9c. Accelerating 329 tons of matter to 0.9c costs, at minimum, 4e22J. As much energy as the black hole itself. Why bother with the black hole, just fire a 329 ton rock. Sure, it's not sub-atomic, but if their ships can withstand 4e22 Joules smacking into them we're at a whole other level.
The Black Hole Space Torpedo Must Be Guided Through Space
To offer an advantage over a directed energy weapon, or a rock, the black hole must be able to deliver its energy over a longer range. In order to have a chance of hitting the target it must be guided, and it must be more maneuverable than the target; a black hole torpedo. This means engines, sensors, not to mention a trigger mechanism and the unobtanium machine to keep it stable, etc... size and weight.
You're no longer firing a sub-atomic black hole at the target, you're firing a small space ship. A small space ship which can itself be targeted and shot down by the enemy's own simpler and cheaper directed energy weapons and railguns. And that is its Achillies heel. Missiles and torpedoes don't make sense in space when you have directed energy weapons and railguns, they're too vulnerable.
You can't hit the ship.