Every time a helicopter is shown in a TV show, the sound used is that for a Bell UH-1 Huey, regardless of whether the chopper is a Huey or not. Therefore it is probably unwise to deduce the model of the helicopter only from this commonly-used movie sound.
Naomi's helicopter crash
The helicopter crashed because of the electromagnetic disturbance created by electromagnetic pulse of the discharge. Since the other electronics and communication equipment, such as those in the Flame, stopped working because of the discharge, it is reasonable to conclude that the equipment in the helicopter failed as well as it neared the Island
The Swan was used to limit the amount of radiation that was emitted, and the electromagnetic pulse could have been a product of the sudden release on that control. The Island could still be oozing enough electromagnetic radiation to have caused the helicopter to crash.
The helicopter experienced the effects of arriving on the Island from the wrong bearing. If the Island is approached from an incorrect bearing, even only slightly, the effect can be catastrophic both to humans and machines due to chronal distortion; that is why we hear an otherwise inexplicably strange change in the speed of the helicopter's blades. The rotor, and all the passengers on board, go through a wave of time distortion. There is no other explanation that explains the sound of the rotor slowing down in four sudden steps (not even the doppler effect) other than time/spatial distortion.
Only Michael (and perhaps Widmore) knew the correct bearing from which to approach or leave the Island. However, this bearing became different since Michael's departure due to the destruction of the Swan Station. This further substantiates the importance of the precision of the bearing that one takes to the Island; if off by only 5 degrees, an attempt to come to the Island at the wrong bearing can be deadly.
The splash seen by the group was not the helicopter crashing (no helicopter was seen), but rather an explosive/missile launched from the Looking Glass: the location of the splash seen corresponds to the location of the Looking Glass, as we have specifically been shown the cable, and no wreckage was seen when Charlie dove in this exact spot later.
We only see limited views and any coral reef ridge could hide the wreckage from site.
The sound when they are around the helicopter in "The Beginning of the End" sounds like a metal distortion flex more similar to the smoke monster than a flex in a router blade or wind blowing through the helicopter. The blades weren't shaking enough to make sound like a thunder sheet (flexible piece of metal shaken as a sound effect for plays)
The skids (metal landing gear) of the helicopter have some shock absorbing springs. Changing weight, such as Sayid leaning in/on to it or wind pressure caused it to rock up and down like shocks on a car
The helicopter that is heard by the group is actually the same helicopter crash of the Oceanic 6 in the season finale. Time is distorted between events on and off the Island, such as the Doctor washing up on the shore before he is killed off the Island "The Shape of Things to Come". Also, there is no mention of there being another helicopter or another pilot by Frank Lapidus or the freighter people.
Effects of the Island
Because time is different on the Island from the real world, the helicopter seems to have vanished.
When Desmond tried to leave the Island, he sailed around in circles for weeks, because he had no idea of any special bearing he was supposed to follow. If Frank turns from the correct bearing, he will end up flying around in circles until he ends up back on the Island. The reason the helicopter hasn't arrived is because it's still in the Snowglobe.
This isn't likely because the helicopter was very low on fuel. If they were to have been circling around, they probably would've had a nice crash landing in the water.
The same effect that caused the rocket to be delayed by ~31 minutes could also cause the helicopter to take longer to get back. The heading appears to be critical to pass through the specific spot toget to/from the Island (referred to as the event horizon in the diagram to the right) This points towards an anomaly w/ a specific point in space, like a wormhole, vrs. a bubble or "snow globe" effect which is 360 degrees around the Island. From the next episode's trailer, it looks as if there's a storm where the event horizon is located which obviously scares Sayid & Desmond. It's hard to tell if they continue through or it made them turn around. There's a brief shot that looks like Desmond attacking Daniel and shouting "I could have been killed!", which would indicate they turned around. They may have crossed the event horizon, got freaked out, then turned back. This could cause them to "lose time" as they were briefly across the event horizon and subjected to the time dilation effects.