Is it true that on D-Day places like Omaha and Utah beach had close to 100% fatality rates within their first waves?
In short: no. Fatalities reaching 100% is extremely rare in a combat situation.
In long:
Of around 156 000 participants in the landings, only around 4 500 were confirmed dead (with another 8-15 000 wounded/missing, depending on the sources I have access to).
One by one:
Utah Beach: 21 000 men of the 4th Infantry Division stormed the beaches in 4 waves, with less than 200 fatalities.
Sword Beach: Combined Allied forces (UK, Polish Army, Norwegian and Free French) landed just under 30 000 people and lost just under 700, with most casualties occurring when attacking inland from the beachhead.
Gold Beach: British XXX Corps landed 25 000 men with around 350-500 fatal casualties total.
Juno Beach: Another combined Allied assault, this time with a lot of Canadian forces included. While they came under heavy fire and took severe casualties in the opening stages of the invasion, D-Day casualties were limited to 340 dead out of 14 000+ landed.
And then there's the big one:
The first wave reportedly suffered about 50% casualties, with about 1 000 Americans dead or wounded.
It's important to note at this point that a unit is considered "destroyed" in most sources if it has lost enough men to become unable to basically exist as a unit. This rarely means every single man was killed or even wounded. Army units, especially modern ones as they were introduced during World War II, depend on a multitude of people in roles other than frontline grunt. Put enough of these people (logistics, technical, officers, communications, etc.) out of action and the unit will seize to exist, especially when combined with a coordinated assault on the fighting forces. This is what is often meant when people say a unit is "destroyed".
And, on the topic of entire units being wiped out, I'm going to put this here. It's a copy of a comment I posted earlier today:
There are very few instances in history where any army lost the majority of their troops in battle.
Some famous examples of armies who lost a battle and the amount of men who died:
Battle of Kursk (Operation Citadel): 780 000 German soldiers with less than 55 000 lost in battle
Battle of the Bulge (Unternehmen Wacht am Rein): German forces peaked at just under 450 000 men, with a maximum of just under 100 000 lost (KIA, MIA, WIA)
Operation Market Garden: 41 500 Allied airborne troops engaged, 17 200 killed, wounded or missing
Even looking at larger theaters, we rarely find a majority of men being killed: over a million men were involved on the Axis side of the invasion of Russia (Unternehmen Barbarossa), with an estimated 250 000 actually being killed.
Complete units being wiped out in battle is a very uncommon if not rare occurrence.
Hope this helps!
Edit: spelling, grammar and lay out.