PLEASE do not listen to the advice some have given regarding silencers. If the developers are inclined, I suggest registering at silencertalk.com and learning some of the facts about silencers and their use.
Raven Shield did infact take for granted that operators would be switching to subsonic ammunition. .45cal with the standard 230gr projectile is subsonic by default, so they did good by not reducing .45 damage [at least very much, IIRC].
As far as I know, in the 5.56 caliber, use of subsonic ammunition is practically nonexistent. Only recently have a couple manufacturers created subsonic loads that will properly cycle the action on an AR-15 [/M16]. For all intents and purposes, the suppressors of the 5.56 caliber are not 'SILENCERS' per se; the super-sonic crack is still present. While the report may still be heard, it is very difficult to tell exactly where the shot came from. This is the main tactical advantage, as well as preserving the operators' hearing for communications purposes. If you want to go subsonic and still take down a target at long range, the proper caliber would be the .308/7.62NATO, as the heavier bullet retains more energy at subsonic speed. Please DO NOT make the silenced 5.56 subsonic as this makes the weapon virtually useless and is not realistic.
In 9mm/.40 and others, subsonic ammo may in fact be used by SF operators on a mission-specific basis, but you can use normal supersonic ammo through them just fine. The silencer its self does not reduce damage -- it's merely the reduced velocity of subsonic loads resulting in poorer penetration and fragmentation issues in the 5.56. Suppressors in fact increase velocity by a few fps, and most of the designs [depending on method of bore alignment/attachment] will improve accuracy a good deal. Ideally, an operator would be using hollow point subsonics in the pistol calibers to effectively negate loss of penetration. However, on 'thick' targets, or angles that require extreme penetration to reach vitals, there would still be a disadvantage. Armored targets, of course, are out of the question for any hollow point or subsonic.
As far as in-game deployment of silencers goes, it should be noted that silencers become Extremely Hot, and while the latest silencers use a variety of 'quick attach' gizmos, to take it off you still have to cool it down before taking it off. Also on the subject of heat -- this restricts the firing schedule of full-auto fire, as the silencer eventually reaches a temp that would cause material failure. This issue is not as much of a factor in [pistol caliber] submachine guns, however, so long as an SMG silencer is used and not lighter-weight pistol silencer. On silencertalk.com and other places you can find info on the capabilities of the various silencers in use real-world today.
Let me know if there are any additional questions. I would love to help this game out and I can't wait to have a real alternative to Raven Shield again!