Seven recon Excaliburs were lost, not twelve.
As for cloaking -- it's clearly still around, since the RF-103 mounts a cloaking device. Anti-cloaking devices are put into use by Confed in Proving Grounds and in WIng Commander IV (the Lance class ships have the ability to see outlines of cloaked fighters on both sides).
From a non-universe perspective, Prophecy was originally to include cloaking, and a scene that explains that it has no effect on the Nephilim -- because of the difficulty in producing a good cloak device in the Vision engine for just this one scene, it was removed and the explanation added to the ICIS manual.