Not family who I am sure you are looking for but
if she married you would need to find the spouse but unless you find the correct marriage or if she died either way she disappears. The 1911 Census will tell you how long married, how many children born and how many died. The 1901 doesn't have that detail.www.familysearch.org
marriages 1867-1901 there are many Johanna marriages in Tipperary but no spouses listed, these would be on microfilm of the Latter Day Saints.
Cappagh was a townland in both S. Tipperary Union Callan
and also in N. Tipperary, Union of Tipperary. A union covered an area of 12 miles that included parish's, townlands, towns/villages from the named Town.
Parish in N. Tipperary was Toem and Isertkieran in S.Tipp
In the 1894 Commercial Directory is a Thomas ONeill listed as a baker/grocder on Bank Pl. in Tipperary
The Cappagh, Thomas is only 50 and wife Kate 40 are too young to be your Thomas and Kate, they would be 78-80 by the 1901 census.
In Nenagh there is a Johanna but she is married, so unless she married her cousin (common) this would not be her.
In the 1901 there is a family made up of unmarried brothers and sisters at 15 Caheernahallia, Cappagh (Electoral District) Patrick 33, Margaret 30, John 28, Johanna 26 (1975), Mary 22 (born 1899) & Julia 21. Not the right Johanna & Mary.
In the 1901 there 3 Mary's 1 aged about 50 living 23 in Friar,Thurles Town, a domestic, unmarried. The others are a widow and a married woman.
You speak of the Tipperary Heritage Center is that the Latter Day Saints or the History Foundation website?
As I was going to suggest the History Foundation for their
birth and marriage records. This is a not for profit but
fee paying Foundation.
170 ONeill's in the one line telephone book for Tipperary and 179 Dwyers, both have many in Nenagh area also Tipperary
Town area and a few in Cappawhite. Too may to locate a few to write too, even more Mockler's, 1 Bray, 12 Furlongs including Cappawhite & Nenagh, lots of Fahy & Ryans's