tl;dr: It's never explained; it's just a continuity/production error that got missed somewhere along the line.
IMO, this scene was one of the (very rare) times the show dropped the ball this season. Matt and Elektra quite obviously face far fewer Hand than they should have, with no explanation why and very little wiggle room for us to insert out own interpretation.
Initially, after having just fought off about a dozen Hand, Matt and Elektra run up the stairs and shut a door behind them, when Matt says there are "a lot more coming" behind them. When they get close to the roof, he claims there are "too many to count" up there. Since we've already seen his ability to count past a few dozen people, he's strongly implying there are nearly 50 Hand closing in on them.
This matches what we actually see on-screen, which includes (by my count) approximately 40 distinct actors dressed in Hand costumes converging on the rooftop, plus 6 Hand chasing behind the two up the stairs
But once the two make it to the roof, we see a total of about 25 Hand on the opposite end of the roof -- about half as many as we'd already seen up there before -- plus Nobu and four Hand coming up behind them -- again, fewer that we'd already seen on screen.
There's no explanation where the rest went, as we don't see any bodies, no additional groups join the fight later on, the police are never seen fighting them off, etc.
In addition, at the end of the climactic fight scene, after having taken out all of the Hand on the roof, there are only about a dozen bodies, all lying at one end of the roof -- where Matt and Elektra never actually reached.
Even if we allow that the fight itself likely went on longer than the on-screen shots, with Matt and Elektra taking out more Hand than the camera shows -- there's no explanation why there were so few of them before and after the fight.