I understand about questionable certificates, i presume you are referring to keche pearls!
Sometimes keshis are passed off as naturals, whether intentional or not. Shell stocks that are hatchery spawned or reared are aquacultural events, so even if they are incidentally or otherwise spontaneously formed pearls, they are by no means natural. For example, even if an animal in a zoo was conceived by natural methods, the offspring is born in captivity, hence not wild. Several countries have standards which imply naturals can only be called as such when they are formed "without human intervention, by any means".
I was taught to look at the structure of the pearls, ie, Natural has onion structure and cultured have not? is this right?
Although there are rare exceptions, almost all pearls have concentric growth. Much like the rings of a tree.
When you say Natural pearls are translucent, are you also meaning Akoya ( sorry for silly question)
Not a silly question at all. In fact, I thank you for it. Personally, I'm not aware of any specific trade in natural akoya pearls and if they exist, they are exceedingly rare or decades/centuries old. Naturals, keshis and freshwater pearls can pass light because they have no beaded nucleus. While opacity is not a single factor for determination, it is a point to add in their determination.
Even a single strand of naturals were likely selected from an enormous pool of pearls. I own thousands of naturals, but could scarcely match enough to make a child's bracelet, which is why I opt for solitare or few pieces in settings.
Regarding the provenance we try and buy from dealers, auctions and privates always subject to certs. But sometimes you may see something at a show or on travels where you have feeling it may be natural, but only experience, knowledge can determine this.
Provenance can come from anyone with reasonable credibility. Certification can be expensive, erroneous and prohibitive. Some labs have gone to great lengths to determine the subtle differences between keshi pearls and naturals, by noting the shape and opacity of the nucleus, but even at best, it can never be perfect analysis. Likewise, these are highly scientific examinations with sophisticated equipment out of the reach of a lay person.
I've seen some shady or grossly insufficient certificates in my day and a whole lot of unfounded claims about pearl origins. Not to mention deliberately misleading or fraudulent assertions. Unless you harvested the pearl yourself, you'll never really know unless your best instincts are coupled with reliable, responsible and objective overviews.