Your initial message confused me as you talk about Michael and Abigail and their son, Michael, but then you talk about Thomas and Johanna and their missing children.
Michael Sr. appears in the 1861 Census in Halifax. It's a head-of-household census only but indicates there are 2 males and 5 females in the house.
The 1881 Census shows Michael, a shoemaker, aged 64, in Halifax, living with Abigail, aged 65. No children left in the household.
The 1891 Census in Halifax shows Michael, a shoemaker, aged 73, a widower, noted as a pauper in the Poor's Asylum. There is a corresponding death record for him on September 4, 1894 in the Poor's Asylum in Halifax, a pauper, aged 77, altho' it says he's married.
1891 Census for Michael Jr. shows him with his wife, Cartha, and children John W., aged 10; Mary, aged 5, Walter, aged 4, and Guy, aged 2.
Did find a reference for Michael & Abigail's arrival:
Name: Michael Gear
Arrival Year: 1845
Arrival Place: Halifax, Nova Scotia
Primary Immigrant: Gear, Michael
Family Members: Wife Abigail Murphy
Source Bibliography: PUNCH, TERRENCE M. Erin's Sons: Irish Arrivals in Atlantic Canada, 1761-1853. Baltimore: Genealogical Publishing Co., 2008. Volume II.