Brian, Yes that's my view on Thomas Looney. All the subsequent data seem to support his parents being Thomas and Margaret Shimmin; note one of his children was named Joshua Shimmin Looney (not conclusive, but suggestive!).
As for Ann Jane Looney, I've drawn a total blank!
Perhaps Ann Jane was b/c under her mother's name and although her parents did not marry, she assumed her father's surname in later life. I've had one ancestor (a Moses Quine) who only officially reverted to his father's surname on his wedding day.