There is a risk/reward aspect with how many you build versus where you position them, etc.
In order to gather knowledge, you must have a command station. In order to have a command station you must have the planet under control. So just position your research station next to your command station under the shield and behind the turrets. Doesn't seem particularly risky, and you still get the full rewards. It's not as though putting my station in a risky position will give me any extra benefits, especially now that knowledge raiding is gone. If, heaven forbid, my research station dies, I'll just rebuild it; they're cheap.
And you actually have to hold the planets that you capture for some length of time, and get the science labs in place and in a location where they will survive long enough, etc. On distant planets that you capture in enemy territory, that can be easier said than done.
Holding planets can indeed be difficult, but by the time knowledge gathering is even and option I've already spend 2 or more minutes building a command station, so holding it for a few more minutes probably wont be much of a concern, especially now that I can build freely on the planet. It could be difficult to move research stations to a remote planet, unless you have transports. If I don't have transports, or can't use transports, I'll just build a new set of research stations at the remote location (after all, I already have a command station there) because research stations are quite cheap.
Also, I don't see any reason to build more than one mark 1 research station. I suppose if your capturing a new planet every 15 minutes you'd have to build a second to keep up, but if your managing to capture planets this fast how difficult is building one additional research station?
This is why having the command stations themselves gather knowledge was suggested, because any time you have a command station it's either never under attack or well defended, and in such situations gathering knowledge is completely trivial.