They were most certainly used, but they weren't necessarily common throughout all of pirate history. There are only two, maybe three, surviving pirate flags bearing the skull and crossbones. All three come from the latter half of the 18th century or later.

You can view them and read about them here:

https://www.bbc.com/news/uk-england-hampshire-16164191

https://www.quora.com/Naval-History-How-do-we-know-what-Jolly-Roger-a-pirate-used

None survive from the traditional Golden Age, although we do have records of them.

The term Jolly Roger usually refers to the skull and crossbones, but it can refer to any pirate flag; usually those flown in Nassau between 1715-1725 or so. The first reference we have of the term Jolly Roger on board a pirate ship comes from A General History of the Robberies and Murders of the most Notorious Pyrates by Captain Charles Johnson.

However, the skull and crossbones comes from earlier sources: as old as the 16-17th century Barbary pirates in the Mediterranean. The color scheme of the skull and crossbones comes from the Barbary Coast as well. Among the first pirate flags of the Age of Sail the best known is that of Hayreddin Barbarossa. It was green and imbued with Islamic imagery; crescents, scimitars, and Quranic verse. However, typical Ottoman naval standards in his navy were a black flag with a crescent and identifying Arabic Script. One could picture the modern day flag of ISIS, which was based on those old Islamic flags.

A ship approached by one of these ships knew they were under attack, and would be forced to chose between surrender, flight, or battle.

The European Barbary pirates of the early 17th Century used mostly national flags, though not from their own nation of origin. They captured Spanish, Venetian, English, French, & Dutch flags to use in false flag attacks. That's the origin of the term 'false flag'. For example, a French ship would often willingly approach a ship with a French flag, and the pirates would hide belowdecks until it was too late to escape. The appearance of the pirates on deck was a declaration of hostile intent. However, that was less than ideal. They had to be close enough to be seen, and that means they were in range of even small arms fire.

One of the Barbary pirates who also operated in the West Indies and the coast of Newfoundland, Peter Eston, is said to have used a black standard and even used a skull and crossbones. The legitimacy of that claim is debatable though.

Later pirates adopted a blend of those tactics. The Buccaneers in the Caribbean and Roundsmen in the Indian Ocean chose to use national flags for deceptive purposes, but they would raise a battle standard when they approached a victim. This was usually a solid red, green, or black flag with a colored outer layer to distinguish ships. Bartholomew Sharp describes battle standards in red, yellow, and green with tassels or embroidery in opposing colors.

It wasn't until the early 18th century that we get common reports of pirate flags with traditional imagery. In Nassau nearly every pirate captain had a distinct flag for their ship and crew. Blackbeard's standard was a horned skeleton wielding a bloody spear. His was one of many Jolly Rogers to utilize a skeleton. An hourglass, blade, or bloody heart were also common imagery.

However, the first Bahamanian pirate to use the skull and crossbones was Henry Avery. He was a Pirate of the Round operating in the Arabian Gulf, Indian Ocean, and off the coast of Africa. His standard was either red or black and had a skull facing right with crossed bones underneath. When Avery fled to Nassau he brought that flag culture with him, and within 20 years nearly every pirate had a distinct flag with the imagery of death.

That was they point. To sail in with a Naval standard, usually the Union Jack, and then raise the Jolly Roger. Most captains that saw the Jolly Roger knew to surrender. They would lose cargo, but not their lives and probably not their ship. It was an intimidation tactic, backed by hundreds of brutal, deadly raids. And it worked.

The second most common Jolly Roger was a modification of the Skull and Crossbones. It was a Skull and Sabers. It was flown by one of the two major factions in Nassau piracy, that group including Charles Vane, Calico Jack Rackham, Anne Bonny, and Mary Read. They chose to use a different symbol in part to differentiate themselves from the group including Blackbeard and Bartholomew Roberts. They weren't outright enemies, but they were definitely rivals.

However, the Skull and Crossbones won out over the other personalized designs. It was internationally recognized, and very clear. It meant death. So eventually Black Bart Roberts, Edward England, Blackbeard, and Stede Bonnett adopted the sigil. Pirates for the rest of the 18th century used it, though not uniformly. It was present during the American Revolution, the Napoleonic Wars, and the French Invasion of Algiers which put an end to Barbary piracy. The skull and crossbones is the symbol that would endure for at least a century, and would go on to be adopted by certain non-pirate naval units in WWII.

Sources (and excellent reading):

Pirates of Barbary by Adrian Tinniswood

The Adventures of C llaptain Bartholomew Sharp by Basil Ringrose

A New Voyage Round the World by William Dampier

Under the Black Flag by David Cordingly

The Republic of Pirates by Colin Woodard

Villains of All Nations by Marcus Rediker

A General History of the Pirates by Captain Charles Johnson

And a little self promotion: you can always hear more about pirates and piracy on The Pirate History Podcast.