So for what it is worth my advice is to experiment with sensor distortion probes. These act like normal probes sweeping away the fog of war and illuminating enemies over a wide area but they have the added advantage of obscuring any of your units within the probes range from the enemies viewpoint until they get very close. It is like stealth mode for your entire fleet. What is not to like?
I have looked over the guides on Gamefaqs and surprisingly none of them recommend this very useful probe. I suspect that this is because in most levels of Homeworld 2 the action starts straight away and continues without let up to the end of the level. You cannot hide units that are already engaged in combat so the sensor distortion probe would appear to be useless.
However it is in just these relentless battles that I find the sensor distortion probe can be invaluable. The thing is that the Vagyr enemy usually attacks in waves. One of the main difficulties of the game is that there never seems to be enough time to regroup and rebuild between waves so the relentless onslaught eventually overcomes your dwindling forces. This is a situation where the sensor distortion probe can really help. If you get a few (two or three may be enough) probes up before the end of a wave to cover your entire force then once the current attackers are eliminated you effectively disappear from the map. You will not be attacked again until you peep outside your stealth bubble. This allows you the time you need to rebuild your forces.
Pressing TAB will highlight the spherical zone around a probe that you are safe to operate in. The Vagyr will send out the occasional scout or probe of their own so be sure to have some fast strike craft on hand to dispatch them before they get close enough to blow your cover. The sensor distortion probes have a wider viewing range than their stealth bubbles so you can always see an enemy coming before they can see you.
It gets even better.
A rather cheap tactic is to send out a roving squad of bombers to take out undefended enemy capital ships while most of your forces are hiding behind the stealth bubble. Carriers make particularly good targets but destroyers and even battle cruisers are doable if they don't have a fighter or corvette escort. Just be careful not to drag the enemy back with you when returning home.
An advanced tactic is to use multiple probes to build a stealth tunnel between your position and an enemy stronghold. With care you can sneak a strong strike force right up to their doorstep and take out shipyards with minor losses.