I've never had any significant problem fighting cloaking ships. Once you know they're there, you have a pretty good idea where they are going to uncloak (e.g. on your tail) so it simply becomes a matter of waiting and dealing with it when it happens. Cloaking usually takes a few seconds, and you can still shoot them if you can predict which way they turn after cloaking. If I was fighing a Dragon in a Vampire, the fact that it could cloak and I couldn't would not worry me in the slightest.
The only time a cloak would be a serious advantage is in an ambush attack (e.g. the opening movie of WC4). In the WC3 approach to Kilrah, I would cloak before the final autopilot to Kilrah (as you're meant to) select full broadside of missiles, fly up behind Hobbes, uncloak and boom! Only Thrak to deal with. Of course, the game itself denies this advantage to the enemy (hmmm, I'm at an empty nav-point, yet I can't autopilot. I wonder what's up?)
Also, I do not believe that Prophecy era ships are fitted with Cloaks AS STANDARD, with the exception of the recon Excaliburs. On a standard carrier fighter, they are usually a waste of money and weight. That doesn't mean that they cannot be fitted with cloaks if and when necessary. However, the early recon missions against the nephilm were most likely conducted by cloak-equipped excals and were unsuccessful, suggesting that cloaking tech is ineffective against the nephilm.
You only see two firing at a time unless you chainlink them to fire all at once.
era seems pretty slim, given that all except 6-10 of them were confirmed destroyed in WC4.