It does look possible that the patronymic form Griffith Humphreys is used in the 1841 and 1851 censuses with Griffith Thomas being used from the 1861 census onward.I don't know if there is a precedent for this.Griffith Humphreys in 1851 and Griffith Thomas in 1861 are both listed as "limer",but the wives appear to be different(?)-Margaret in 1851 is listed as born Gwyddelwern,Merionethshire and Mary in 1861 as Llanfihangel,Denbighshire.It is this that needs resolving to be sure.
There is Evan Thomas Humphreys(b.1838) in 1851 who may incorporate this duality.I think he appears in 1861 as Evan Thomas,also a limer, at RG09/4308/45/19.I believe his sister,Elizabeth is on the same page,having married a RIchard Jones in 1854.The John Jones(grandson)may be theirs.
Regards
Roger