Yes I've seen most of this - too many pieces of the jigsaw, and too difficult to put them all together into a coherent whole!
There is no doubt there was a close connection between the Hydes and the Hursts (And the Wards). In a small community at that time, it would seem they were of a similar standing, although I think the Hydes must have been the more high status family. They certainly intermarried.
I see looking back at the notes I made over a year ago, I decided Ann the wife of Thomas Ward was not Ann Hyde son of Robert. This Ann Hyde married Ri(chard?) Risley, gent, 11th Sept 1593 at Stockport. The entry actually says she was the 'daughter of Robert Hyde of Northburie esquire'.
So bang goes that theory!
You say "Henry, Katharine, Ann and Hamnet are certainly Katharine’s children, based on her will, and there should be an Ellin, too.", but I can't see that she mentions 'my son Henry' anywhere in it.
Katherine (daughter) is married to (John) Lamb + 5 children; Ann is married to William Williamson: Hamnet is executor (wife not mentioned); and Ellin is married to (John) Stanley. Henry's children Henry and Mary are mentioned as her grandchildren, but Henry not mentioned as her son as far as I can see. I wonder why he was not executor, as 'eldest son', instead of Hamnet. Perhaps I'm reading too much into it.
Henry is classed as 'my eldest son' in Henry's will of 1651. Doesn't say who his mother was though. Both 'Hamnitt' and Ann are not yet 17 years old and Henry his son has not yet got any children.
I think you're right that the 'Hyde alias Ward' comes from a previous generation somewhere.
There is a document at the Court of Star Chamber at National Archives.
http://discovery.nationalarchives.gov.uk/details/r/C3163529Robert Hyde versus Thomas 'Hide' alias Ward and others re Forgery of a feoffment of a house and land at Northbury.
The date of it is actually 1579. It is many pages long, but mentions these children of 'Thomas Hyde alias Ward' as to whom property should be left - 'John Ward his sonne' (by this stage, some pages down, Thomas Ward (alias Hyde) the father is now referred to as just Thomas Ward); 'Thomas Ward another sonne'; Alice Ward daughter; and Ann Ward another daughter. Then interestingly, if there is no issue from any of these children, to 'Hamnet Hyde sonne and heyre apparent of Robert Hyde Northbury Esquyer'.
It is pretty tricky to transcribe and the images I have are not wonderful, plus the terminology make it somewhat difficult to understand.
Initially I thought this was our Thomas Ward, but now I think this Thomas must be the FATHER of Thomas married Ann, and grandfather to Katherine, Hamnet etc born in the 1580s and 1590s.
Here is proof of siblings Alice and John of the marriages at Poynton and Adlington.
So it is THIS Thomas who starts the 'Hyde alias Ward'?
By the way, if you haven't come across the National Archives Discovery website you should look at it. A treasure trove of goodies.
You'll spend hours finding exciting documents etc! well, the short precis for them at least.
Always another avenue to follow in family history!