I'm really surprised no one else has posted this here, considering I know I am only one of many frustrated people experiencing this.
Are you aware that pop-up dialog boxes break your cloak, regardless of the context or situation? I'm talking nearly every pop-up dialog in the game. Talk to your bridge officers? Cloak breaks. Get hailed by someone? Cloak breaks. Mission is progressing and the game just wants to let you know? Cloak breaks.
And the cloak breaks on a bunch of other things, too. Loot notification? Cloak breaks. Scan that thing over there? Cloak breaks. Beam up / down? Cloak breaks. Sometimes, I'll just randomly decloak for no apparent reason whatsoever. I can't even begin to tell you how annoying this is, especially in PvP war zones such as Kerrat. I understand this is a bug that has existed for nearly two years now? Why is nothing being done about it, and why is it that people are saying that it got even worse after one of the January patches? I'm not trying to be sarcastic - I only finally started playing with a cloak-capable ship last month - but I see why people are complaining, and why your sales of cloak-capable ships in the C-Store are probably less than they could be. It definitely does not give me much incentive to buy the new Bortas when it comes out if everything I do is going to force it to decloak.
For the record, the bug affects both Federation and KDF ships of both cloak types. And no, this is not the way it worked in the show - cloaked ships only ever had to drop cloak to attack.
Yes. Also its canon to drop cloak for transporting. I would think it to be bad idea to scan whilst cloaked. Think of it as a big over here sign. I would think scanning to be simular to a submarine ping.