Caution, Daredevil Season 2 spoilers below.
In "The Dark at the End of the Tunnel," the Hand clearly know that Daredevil is blind. They explicitly hold their breath and don't use weapons so that he can't track them. Previously, they had simply been stopping/masking their heartbeats.
STICK: Listen very carefully. You've been tracking their weapons. So they dropped 'em. Tracking heartbeats is kids' stuff. Time to go deeper. Track their breath. Sooner or later, they gotta... (exhales deeply) exhale.
In the earlier episode "Guilty as Sin," we see a ninja watching Murdock's apartment as Daredevil, Stick and Electra enter it, so they could deduce his identity by this point, at least.
Were they masking their heartbeats before they knew he was blind? If so, when did they figure it out?