Yes, the ODS do work in both UCCE and UCCE v2 (which I just tested again). The issue is that they are moving so far around the planet that their target acquisition matrix will reset quickly because they do NOT stop to fire - and they will NOT fire if they don't have a near perfect solution. Especially those that use missiles instead of guns/turrets. In fact, they were more powerful back in UC, but I think since UCAWA I tweaked them and that carried on to UCCE.
Capital ships only cloak when conditions warrant it. Seriously, who hasn't run up against cloaked ships?
Capital ships only use missiles when conditions warrant it. The reason being that depending on the range, target type and the target priority, they will use their more powerful main guns and turrets. Also, it is more efficient for them to launch fighters than directly engage high level targets (e.g. stations, other cap ships)