When I did this back in the day, I would siphon as regular with the end tube going into a net, with the 5 gallon bucket underneath. I would do it as quickly as possible to limit the stress, and any that got sucked up went into the net. When I finished vacuuming, I simply returned them to the tank since they all landed in the net. Siphons usually have a lower end water flow so they didnt get hurt, but I still didnt like doing it. It was the only way I could think of at the time.
Recently I did something similar at work. I used an old net and cut out the mesh, then I affixed it to the end of the vacuum with a rubber band. It wasnt as effective at getting the larger debris, but it didnt suck up any of the babies either. The finer dirt particles got sucked up no problem and I just have to clean the tank more often.