16th century sources do indeed tend to be pretty unclear when it comes to firearm's rate of fire. Humfrey Barwick was a strong proponent of firearms at the end of the century and as such is probably represents the upper end of what might be expected in terms of fire rate. While serving as a mercenary for the French army he described a war meeting in which he overheard a nobleman claim that an arquebus could only be fired 10 times per hour. Some people apparently did think the fire rate was this low, but Barwick thought the man was daft and afterwards approached him offering to personally demonstrate shooting 40 times in one hour with a single piece. One shot every 1 minute and 30 seconds doesn't seem like much, but this seems to have only been the rate for long term fire over the course of an hour, which would have required occasionally cleaning the weapon, adjusting the match, and measuring the powder for each shot independently since a soldier at the time typically didn't carry 40 whole wooden cartridges at a time.

For short term rate of fire, later on in his discourse he described the maximum number of times that a soldier with a musket could shoot at an advancing army, which involved shooting once in the time it took the enemy to march (not running) 80 yards (presumably 60-90 seconds, he recommended making up the difference by shooting multiple bullets at a time as the enemy got closer). The fact that he says this is for a musket is significant because the 16th century musket was a very different beast compared to the muskets of the 17th and 18th centuries. It was extremely heavy with a longer barrel and a larger bore than later weapons and had to be supported by a forked rest while firing. Most troops at the time would have been armed with an arquebus or caliver, firearms which which were much lighter and had a much shorter barrel. Humfrey Barwick and Sir Roger Williams both wrote that the arquebus/caliver could fire twice as quickly as the clumsy musket could (though they prefered the latter because of its far greater force).

That would make the ideal rate of fire for the late 16th century arquebus/caliver: 30-45 seconds per shot max, 40 shots per hour sustained

And for the heavy musket: 60-90 seconds per shot max, 20 shots per hour sustained.

As far as how rate of fire compares to the wheel lock or flintlock. A matchlock is generally more complicated to load since it requires constantly tending the match to keep it burning as well as adjusting the match length as it burns down. In addition manuals on loading reccomends removing the match after every shot and holding it in the opposite hand so the soldier doesn't accidentally blow himself up while handling powder (loading could still potentially be done much faster if shortcuts are taken as demonstrated by this reenactor with an arquebus). A wheel lock firearm did away all this but added the need to reset the spring with a specialized tool after every shot. As far as flintlocks go, most manuals and sources tend to give a maximum fire rate of around 3, maybe four shots per minute. As far as I know, even with greatly simplified drills reenactors tend to have a lot of difficulty reloading a full sized Napoleonic musket in under 20 seconds.

So to sum up, 16th century muskets did take a long time to reload, largely due to its size. A flintlock musket was generally quicker and easier to reload than a 16th century matchlock caliver (which was similar in length and weight) though probably not as much as you're saying. And there was more to reload speed than the type of lock.