I don't have any additional information on Thomas' parents, John and Dinah, other than what I found on that website link earlier tonight.
As far as I can tell:
Dinah, Deanna and Hannah are all the same person. Dinah and Deanna are shortenings of Diana-Hannah, her actual name.
According to this site, John and Mary, his second wife, had 4 children (although you obviously have discovered others):
Sarah 1828-1846
James 1831-1869
Anne b. 1832
Henry b. 1835
John Cupper b. 1791.
Dinah (Diana-Hannah) Cupper 1783-c. 1819
Their children:
William Cupper b. 1812
John Cupper b. 1813
Elizabeth Cupper b. 1815
Thomas Cupper b. 1820 -- Dinah (according to the site) died c. 1819, so this date is not necessarily exact (perhaps she died in childbirth??)
Once again, almost all of this information comes from linked site which I only found tonight, and so I can't assure its accuracy. In terms of actual records, you seem to have the actual records, which I only have a couple of through look-ups that kind people on this site have given me (you actually have some dates and information that I do not have, so thankyou!

)
I hope this helps,
C. Rodda.