From what survives of the mined amethyst it appears to mainly have been used for jewelry beads in the Middle Kingdom. They had a huge bead industry so presumably there would be a demand for minerals as semiprecious gems irrespective of any religious significance added on to them. Other than beads there are some stone vessels form the Predynastic and Early dynastic periods and some amulets during the Old Kingdom. As for religious meaning, the ancient Egyptian word for amethyst is hsmn (the h has a period under it). The Wadi el-Hudi area was called the "land of hsmn" with the patron deity as Hathor, called "lady of hsmn" from stelae found in the area (Aston 1993).
Aston, B.G. (1994) Ancient Egyptian stone vessels: materials and forms. Heidelberger Orientverlag, Heidelberg, 196 p.
Archae Solenhofen (solenhofen@hotmail.com)