How would you determine which men have joined the pirates?

Silver's men would look to him for council. It would take a lot of observation, a lot of listening. Men conspiring in such a small area would be easily spotted in time. This is confirmed in Chapter Thirteen.

If the conduct of the men had been alarming in the boat, it became truly threatening when they had come aboard. They lay about the deck growling together in talk. The slightest order was received with a black look and grudgingly and carelessly obeyed. Even the honest hands must have caught the infection, for there was not one man aboard to mend another. Mutiny, it was plain, hung over us like a thunder-cloud.

And it was not only we of the cabin party who perceived the danger. Long John was hard at work going from group to group, spending himself in good advice, and as for example no man could have shown a better. He fairly outstripped himself in willingness and civility; he was all smiles to everyone. If an order were given, John would be on his crutch in an instant, with the cheeriest "Aye, aye, sir!" in the world; and when there was nothing else to do, he kept up one song after another, as if to conceal the discontent of the rest.

Of all the gloomy features of that gloomy afternoon, this obvious anxiety on the part of Long John appeared the worst.