This unit can fire both types of missiles. Tactical missiles are built and launched automatically, but strategic (long range nuclear) missiles must be constructed before launching. In Forged Alliance, strategic missiles can be built while the sub is moving, so it is wise if your economy can handle it to begin building these missiles right away. Because of the long build time, it is now unwise to assist a strategic missile sub in building its strategic missiles. Think of the sub as a mobile strategic missile silo, much less vulernable to gunships and bombers, and a lot less likely to be discovered if hidden, but also able to support other units with its high-damage tactical missiles.
Strategic Missile Submarines have a high amount of health, can withstand quite a beating against an enemy navy when submerged, and can hammer a sea or land force from a very safe range. However it is not recommended to allow them to take on an opposing navy on their own in the open water, as their top speed and acceleration is the slowest of all naval units, and that will quickly bring the Strategic Missile Sub within counter-sub weapon range. As with all submarines, if you need to improve its speed simply surface the vessel to gain a speed advantage, although this makes it more vulnerable to surface fire.
Strategic Missile Submarines do not need to surface to fire their Tactical or Strategic missiles. Tactical missile defense units can stop its tactical missiles, but they have no effect on its strategic missiles. Conversely, strategic missile defense units can stop its strategic missiles, but they have no effect on its tactical missiles. A Strategic Missile Subs nuclear payload has a slightly lower inner damage than a traditional nuclear silo, however this will only matter to surviving experimentals. The cost per second in energy is slightly smaller than a traditional Strategic Launcher, but the build time is two minutes higher.
Do not underestimate these submarine's tactical missiles. While their purpose is quite obvious: a fast-to-build, watered-down, hard-to-notice strategic missile launcher, its tactical missiles can aid in any type of assult as long as you can put the submarine in range of an enemy base. The missiles have a DPS of 200, have absolutely no build cost, fire automatically, and will make short work of any un-shielded target. Despite their efficiency, you should not build Strategic Missile Submarines for the sole purpose of a submersible tactical missile launcher because of their extreme costs (for a tactical missile launcher atleast). Please note however that if you desperately want water-borne tactical missiles, Aeon have the Torrent Class and UEF and Seraphim have their Cruisers. The tactical missiles on subs are nonetheless still a great addition due to their high damage, but should be regarded as secondary to the nukes.
The Cybran Strategic Missile Submarine is the only one of the three to have torpedoes - allowing it to combat other subs. It also has the longest build time, the longest range (for its tactical missiles) as well as having the least health and a quite comical name. The UEF Strategic Submarine has the most health, with the Aeon Sub falling in between the other two - arguably making it the worst of the three, purely statistics-wise.
However, looking at the effectiveness of the tactical missiles, the Cybran missiles have the largest blast radius, with the worst accuracy, the UEF missiles have moderate blast radius and moderate accuracy, and the Aeon missiles are the most accurate and have the lowest blast radius - giving them each the traditional values of the races' long-range ordnance.
The Seraphim do not have a Strategic Missile Submarine, but their T3 Battleship can fire Strategic Missiles - giving it a similar role, but it takes an extra minute to purchase a missile. The battleship is, of course, a battleship - meaning that it is designed for firefights, having long-range, high-damage cannons.
Thus, in studying all of the statistics, the UEF Ace is an altogether superior counterpart to the Silencer, as it has more health and has 1.5 times the radius of its cruise missiles.
The Plan B costs 10% more resources and build-time, but has the largest radius and range of its cruise missiles (which split into sub-missiles when traditional TMD strikes it) plus a decent torpedo system. Its nukes also include EMP properties present in all Cybran strategic missiles. Thus, for the cost of health and resources, it is more offense-oriented, despite the name.