A Helpful Guide to Guns in Fiction, Part 1

Subsonic Ammunition

This label is frequently bandied about as a magic type of stealth ammunition. Subsonic ammunition does not have the associated "sonic boom" that super sonic ammunition does. This can be achieved with a heavier bullet (the part that actually shoots out of the gun, the whole thing is a cartridge) and/or with a smaller cartridge load. As an intelligent person might suspect, like most "stealth" bullets these don't work the way they are often portrayed. Things that would be helpful to know.

1. Many pistol rounds are already subsonic in most of the loads they are normally fired in. The .38 special for example is ~300 m/s while the speed of sound is ~340 m/s. They still make noise.
2. The subsonic designation is only useful for rounds that typically sit right around the speed of sound for normal loadings. Such as the 9 mm Parabellum round. It can go from 400-300 m/s. For this round, there is a difference in noise between different types of rounds, but they never make a "whisper". There is always going to be noise. They just do not make the characteristic ballistic crack.
3. Subsonic variants of ammunition always have shorter effective ranges than their supersonic equivalents and frequently will have less penetrating power. This is because a slower moving bullet will not travel as far before it is noticeably effected by gravity and experiences significant drop. This might be offset some by a heavier bullet holding more energy.
4. Some cartridges would never be loaded to be subsonic in anything but practice rounds. A .357 magnum round for example. It is well above the speed of sound ~400 m/s and was designed to be so. It would be possible to load it to be sub sonic, but in practice it would be easier to simply get a .38 special round, which will fit a .357 magnum chamber and is already subsonic. This is not to say that people haven't, just that it does not make sense for your military black ops guys to do so.
5. Some automatic and semi-automatic rounds may have trouble with subsonic cartridges. This is because the energy to cycle the weapon for the next shot comes from the cartridge and subsonic cartridges usually have less energy. It is probably safe to assume that your characters have tested their weapons with the ammunition they plan to use off page and so this may not be a problem, but it is something to be aware of.
6. Rifle rounds will never be loaded with subsonic rounds (at least modern rifles, black powder rifles are a different story). It defeats the purpose of a rifle round. Rifles typically fire bullets going 2-3 times the speed of sound. Reducing their speed below the speed of sound reduces their energy by at least a factor of 4 (energy varies with the square of the velocity) and similarly reduces their penetrating power. There is no reason that anyone would do this. They could get a submachine gun or pistol that would be just as deadly, have the same range, be lighter, and have easier to handle ammunition. This includes assault rifles such as the AK-47 and M-16. Again, you can find people that have done this and even people that make subsonic rounds for those weapons, but they do not function like a normal rifle and you can expect problems cycling the weapon with loads that have been so far reduced. Also, the sights for those weapons would be based upon the higher velocity so range adjustments would be unreliable.
Note: There are some types of rifle ammunition that are designed to fire subsonic rounds or even pistol rounds. The subsonic rifle cartridges tend to have much heavier bullets than their supersonic counterparts and rifles that fire pistol ammo are designed for higher accuracy and range with the pistol ammo. And there is nothing wrong with them, but they would not normally be labeled "subsonic ammo". A possible exception to this is the .300 Whisper, which can be either supersonic or subsonic variants. However, subsonic variants weigh nearly twice as much and deliver less than half as much energy. It depends upon making a large hole rather than going deep and delivers as much kick as a .45 handgun round.
7. To give an idea of the impact of subsonic rounds consider two rounds, one that is just barely subsonic at 340 m/s (depending upon the air conditions this may or may not be subsonic and even this close to sonic speeds you are likely to get some ballistic crack) and another that is a more standard M-16 round going 990 m/s. Both are fired at a target on level ground 100 meters away. It takes the 340 m/s round 0.294 seconds to reach the target and in that time drops 0.424 meters (about 16.7 inches). It takes the 990 m/s round 0.101 seconds to reach the target and in that time drops just 0.0500 meters (about 1.97 inches). If you're going to be off by 2 inches on a shot, you don't need to correct to hit your target, but 16-17 inches requires adjustment that can be difficult. Additionally, the longer flight time allows more time for crosswind to effect the shot and drag would slow the bullets causing even more drop. Subsonic rounds are only effective at short ranges. At ranges shorter than 50 meters, the drop is less than 4 inches and could be considered reliable in hitting targets. Note, bullet drop is not the only measure of problems that can be encountered and many rifles have sights to account for bullet drop.
8. Similarly, if a target is hit by the subsonic round in the above example, a standard bullet proof vest would likely stop the round. The standard round penetrates a bullet proof vest.
9. Snipers would NOT use subsonic rounds. Subsonic rounds are for short ranges, snipers need accurate fast moving rounds so they can hit from far away while staying hidden (see number 7). This is a personal pet peeve, a sniper in fiction on a roof a block away using subsonic rounds so they cannot be found and shooting people right and left. If they are close enough to be using subsonic rounds, then they are not really a sniper, but a concealed shooter. Military sniper rifles require all rounds to be put into a one inch circle at 100 meters and this is not possible with subsonic rounds.

Hopefully this has been helpful for your writing. Other topics that will be covered. Bullet penetration (including vests and bullet proof material). Rifles versus pistols and an explanation of caliber.