Especially if you bring along an engineer and some protecting ships, I have gotten along with bringing around 6ish of the mark I labs that are faster. That lets me spend the least possible amount of time on the planet, basically only 2.7 minutes. If you bring more mark I labs then you spend even less time there. The less time you spend, the less time there is for pursuing starships to catch you, snipers to shoot you, etc. Then you just load the transport back up and hightail it out of there, repair briefly if there is a need for that, and move on to the next planet, etc.
I think that Cloaker starships may be easier to manage with just a few labs, but honestly I prefer transport approach because it's so much easier to get past the initial wormhole defenses without having to do a bunch of fighting.
It's not possible to pause science labs, as you say -- there are plenty of ships that can't be paused. But, you can put them inside a transport if you want, which means that they will then use no energy while inside it (though of course the transport uses a fair bit).
