Considering the riches many Conquistadors acquired from the conquests of South America, did pirate attack or raids often occur on ships transporting the wealth back to Europe?
The French corsair Jean Fleury, sponsored by Jean Ango of Dieppe, launched a succesful attack against Hernán Cortés' treasure fleet capturing 2 out the 3 ships with the treasure of Moctezuma, which was substantial. This capture funded a number of French exploratory expeditions and the gorgeous Manoir d'Ango in Varangeville sur Mer, close to Dieppe.
After this, the Casa de Contratación de las Indias, in Seville, suggested the creation of a protection system to the Council of the Indies, which acted immediately. The Council opted for the creation of what is known today as the Fleet System, a yearly convoy that would depart from Veracruz, get final supplies in Havana, and sail for Seville with some heavy armed escort. The system lasted for 250 years and was extremely succesful.
The convoy would be composed of the sgips sailing from the Indies to Spain, protected by four armed galleons: one at the front, one at the rear, and one on each side. The sheer size of the convoys (depending on the year, it varied between 45 and 100 ships) plus the armed escort guaranteed safe transport to Seville.
Only twice was a whole fleet lost: the first time was in 1626, when the Fleet suffered a hurricane, leading to the convoy being scattered, an opportunily craftily seized by the Dutch privateer Piet Heijn, who managed to capture a formidable treasure, appraised by the governing board of the VOC at over 11 million guilders. That year, the dividens paid by the VOC exceded 50%. Piet Heijn's career did not last long after that.
The other time was in 1714, when the Fleet was at anchor at the bay of Vigo. The captured treasure was important, and even led to emmission of commemorative coins with the text "Vigo".
But what happened to the pioneer of these shenanigans, the famous Jean Fleury? His privateering career lasted for five years after his great capture of Cortés' treasure. He was eventually found, taken prisoner by the Spanish commander Juan de la Rentería (son of the renowned Machín de la Rentería), put to trial in Seville, and sentenced to death. He was hanged in Mombeltrán, in today's province of Ávila. Juan was promoted to general, and received and an augmentation of honour to the coat of arms that had been granted to his father. The coat of arms can be seen in the façade of his house, known today as Kapitain Etxea (the Captain's House) in Errenteria.
There were occasional attacks on the Fleet, but mostly unsuccesful. Only 3% of the ships of the Fleet were lost during its duration. Attacking the Fleet was not quite a wise move.
Edit: Jean Fleury had quite a sizeable fleet according to a report from the Casa de la Contratación from 1523. I translate:
"First, a big long-ship of 102 tonnes, equipped with a 102 men, half sailors and half for war. It is equipped with 20 metal artillery pieces. He also has iron artillery, ammunition, and supplies in good quantity.
A ship made in Biscay, taken by the French.
Another ship of 101 tonnes, made in Brittany
Another 5 galleons, the largest of which is of 70 tonnes, another one of 60, other one of 50, other one of 40 made in Biscay, equipped with 200 men of war, that are soldiers who were in the siege of Fuenterrabia"
It was definitely not the classic image of a pirate with his own little ship, but rather a captain commanding a small but strong naval force.