is there any preference for a mezuzuah case that is clear ( so you can see the parchment) or non clear? Or makes no difference?
There is a preference to having a mezuza with a clear case, because then it is possible to see the name ש-ד-י, of the mezuza. If the mezuza is on a doorpost where there is suspicion that unclean things will be done in front of it, i.e. someone not dressed modesty, or babies diapers that are changed there regularly, then it should be wrapped in plastic, with the intention of the plastic being a second covering for the mezuza, and then it should be placed inside the cover.
Lasiv v’chasima tova
Rema Y:D 288-15, Taz 286-5, Chovas hador 1-7.