Whoa! Classic book there. Thumbs up for reading Conan Doyle.
The just so often refers to the as often at the start of the sentence. The idea is that each time Kate Fox makes this motion with her hand there is a rap noise heard.
So hand motion one two three times. Then rapping noise one two three times.
Hand motion once. Then rapping noise once.
And so on.
The notion of a seance may not be familiar. When the cited book was published, there was a fashion for a particular kind of gathering. The usual pattern was for a group of people to sit at a table and join hands. Then the leader of the seance, often called a medium, would perform some sort of ritual intended to indicate summoning spirits. Then there would be a series of demonstrations that the spirits had been summoned.
Part of that demonstration was often the answering of questions that supposedly could only be answered by the spirit of the dead relative. This would often involve a series of methods such as cold reading. And the answers would often be given through rapping sounds.
The usual pattern was that the medium had one or more assistants hiding nearby, and they would provide the rapping noises. Or that the seance leader had a variety of devices concealed under the table and so on. Then during the seance the medium would pull levers or strings etc., and thus make the rapping noises.
In some cases these were harmless entertainment. However, in other cases they were cold blooded scams. The notion was that the spirit of the dead relatives of the people at the seance would come and give them instructions. Take money out of the bank and await instructions. That sort of thing. Then the medium and his accomplices would scam the victims out of their money.