Just how many times have they been discovered and destroyed?
It happened Oblivion, and the second time in Skyrim.
More than that, Cicero's journal mentions that every sanctuary in Cyrodiil was put to the sword.
Their so called secrecy and operating in the shadows isn't much to talk about, either. In Oblivion, one of the members comments that the count of Cheydinhal knows the location of their hideout, but is paid and coerced to keep his mouth shut.
And of course, Commander Maro. When you talk to him after killing Astrid, he tells you he already knows where the sanctuary is and even the password. That is ridiculous.
It seems they are rather overrated as an organization.