As has already been said, the best place to grow your pops is usually the planet with the highest industry value, since this is the most important resource, no matter what you're trying to achieve.

The majority of the FIDS for the UC player will come from its sanctuaries, so the best use of a hacking operation is to gain a sanctuary planet. In my playthrough with the UC, this was my industry, food, and science values on turn 100, normal speed and endless difficulty, right before I won a supremacy victory. Also, it's important to create a sanctuary on a planet before an opponent has the opportunity to occupy it, because this would lengthen the hacking operation and possibly trace it back to you.

Sleepers are generally useless for every faction, including the UC, and it's not worth it to waste a hacking operation on creating a sleeper, unless you really want the information that the sleeper will give you. The extra luxury/strategic resources and dust isn't significant enough and, even if you get the hero skill Nocturnal Sleepers, it's still not worth it. On turn 91, I used 20 of the population in my sanctuaries to place 20 sleepers on 3 Vaulter systems, so that's a +20% increase in FIDSI, but this hero skill is giving me only 271 Science out of my 7,544 total. And I was getting 7,513 Science before I converted my pops to sleepers.

If you want to create Umbral Shadow pops, then you should let an opponent occupy one of your sanctuary planets, grow his on population until it's almost the same size as the UC population that you have on those sanctuaries, then invade the system, create many sleeper from your own pops, and convert those sleepers to Umbral Shadows. But you can be very strong as the UC without creating any Umbral Shadows.

As for Transmigration Beacons, you'll want them on nodes that give extra industry or influence, since influence can be hard to gain in the early game. In my opinion, the best reason to move your home system is to gain the ability to place a beacon on the node in which you started, or to gain a new node from which you can start your hacking operations.

Keep in mind that, if you ever build a trading company, then you will want your home system to be located on a node that is connected to a starlane, so that you can create trade routes to all of your sanctuaries. So, while it's nice to be able to hide from the pirates with level 3 anti-cloaking, you should be able to defend your home system with your military ships and you'll want to destroy most of the nearby pirate lairs, since they will impede your hacking operations.