I wanted to read Wendy B. Harte's contributions to Who Killed Albus Dumbledore before answering this, but it has to be purchased and doesn't have a free preview. Hopefully I won't provide anything out of context.
Wendy B. Harte writes:
Both books contain many series clues, and both were written for charity.
I've read all three of these books numerous times -- to be honest, I don't see "many series clues" in Quidditch Through the Ages (QTTA) or Fantastic Beasts and Where to Find Them (FBAWTFT). Unsurprisingly, clues and resolution come mostly from Tales of Beedle the Bard (TBTB). It's got a lot of good info in it.
In QTTA, in the section about the Golden Snidget/Snitch, there is no mention made of any kind of compartment or space in the center of the Snitch's body where a small object could be concealed. It does say that the Snidget is a certain weight and the Golden Snitch was created at the exact same weight as the Snidget -- we don't know if Scrimgeour weighed the Snitch Dumbledore left to Harry, but had he, because of the Resurrection Stone inside, perhaps there might have been a weight discrepancy which would've confirmed to Scrimgeour that there was indeed something inside the Snitch.
In FBAWTFT, the Demiguise is listed and it is mentioned that Demiguise hair can be used to spin invisibility cloaks; however, there is no specific information about invisibility cloaks as there is in TBTB, i.e. the difference between a Demiguise-spun cloak and a cloak gifted by Death himself.
There is a large section on dragons (Triwizard Tournament; Norbert; escape from Gringotts) but, again, it's not specific to the story. The Erumpent horn is mentioned (Xenophilius Lovegood) in a general manner. Phoenixes are featured and it is noted that Phoenix tears have healing properties. I'm pretty sure Chamber of Secrets had already been published by 2001, though.
So as far as QTTA and FBAWTFT go, I would say that no, they do not have clues hidden in them. They were mainly written as a comedic endeavor for Comic Relief. They're more fanciful than TBTB.
TBTB answered a few questions. For example, the Avada Kedavra, Cruciatus, and Imperius curses weren't sanctioned as "Unforgivable" until 1717. We learn Sir Nicholas's backstory. We learn the first of Adalbert Waffling's Fundamental Laws of Magic: Tamper with the deepest mysteries -- the source of life, the essence of self -- only if prepared for consequences of the most extreme and dangerous kind. Wizarding portraits are explained. Animagi are explained a bit more. There's a paragraph or two on invisibility cloaks -- they are not generally infalliable, etc.
So I don't see either QTTA or FBAWTFT as having clues to the series. TBTB does, of course, but as Tony Meyer mentioned, it was published after the series was complete.