Thutmose III was Hatshepsut's stepson, his father was Thutmose II and his birth mother a royal concubine (shades of Dune, eh?) because Hatshepsut bore no male children. After Pharaoh died, she assumed the role of regent, and then Pharaoh, ruling Egypt (apparently quite successfully) until her death, when her stepson ascended the throne as an adult. Why he waited so long after her death to "erase history" we will probably never know.

My guess is it probably was for political reasons. Hatshepsut had a natural daughter with Thutmose II, perhaps she was still alive and making a claim on the throne; it could certainly be argued she had precedent. Evidence of a successful former female Pharaoh may been embarrassing or threatening to Thutmose III.