Ah, a fun question.
First, there is the fact that the league itself disappeared. This tips Jabez Wilson off that something is wrong, and leads to the second clue: the existence of the league itself, which is a bizarre thing.

Now, once Holmes is on the case, quite a few clues are spied that Holmes relates to his overall knowledge of London (criminal) society and human nature in general.

Wilson's assistant is too smart for his position; why does he keep it?
His assistant pointed out the position to him; why?
The strict rules keeping Wilson in place during his work are a clue; someone wants him anchored in place.
When Holmes hears what Vincent Spaulding looks like, he recognizes him. This is a major clue, since he recognizes him as John Clay, a criminal.
Spaulding's knees are dirty, indicating he'd been digging.
Then there's the location of Wilson's shop, which is right against a bank.
Holmes thumps his stick against the stones and hears a hollow underneath.

Together, he deduces what they are up to.

Greg