Like other RTS titles, Star Trek: Armada has detector game mechanics. Some units can make themselves invisible by means of a Cloak. This means, the unit is invisible for normal sensors until the Cloaking Device is turned off. As such an ability would be game-breaking without a counter measurement (a player would have to just not decloak and the match could never end), the game also provides for detector units and stations. Both use the Tachyon Detection Grid, which allows so see cloaked units. Ordinary stations and ships will not be able to see cloaked ships, which in turn allows cloaked ships to start surprise attacks.
The optical difference between cloaked and uncloaked units of this is shown here:
On the left hand side you see an uncloaked Vor'cha unit. On the right it is shown with its Cloaking Device active. The cloaked ships are a bit brighter and slightly transparently depicted than normally.
Cloaked ships will not automatically fire their conventional weapons. Otherwise their cloak would be rather useless. If you successfully order a cloaked unit to fire on a target, it will automatically decloak. An active Cloaking Device also shuts down the shield generator subsystem. Therefore cloaked ships are very vulnerable against beam-ins and damage dealers. This is the main drawback of the cloaking mechanics. An attacked cloaked ship will automatically decloak as well. Many special weapons do allow for forcing a decloak, e.g. the Sensor Jammer, but not all of them do. Some of them can even be used without turning off ones own Cloaking Device (e.g. Gravity Mines).
When playing with the tech tree No Special Weapons, the description is actually not entirely accurate. Technically speaking, the cloak is also a special weapon, as well as its counter, the Tachyon Detection Grid. But both are very much in use. The detector units and stations all automatically use the detection grid and all ships capable of conventional cloaking can do so.