Well it is possible to hydro lock an engine with a CAI assuming the intake cone is in a position where it can easily be done. A friend of a friend of mine had an R32. he ran the piping of his CAI into his front tire well and when the next rain storm came he hydro locked his brand new R32. If you buy a cheap intake for your car you will certainly increase your chance of hydro locking your engine. One of the nice things about a lot of good intake systems is they come with heat shields which can also act as a splash shield. The Conforti intake system i plan on buying for my car actually has a shield made of a heat resistant plastic which helps keep the intake air cool and because it is form fitted to seal off the intake cold from the engine bay it also is designed to fit flush with the hood when you are not showing off your engine bay.
This is a link from Turner Motorsport showing the Conforti CAI
Turner Motorsport - Item# JCINTAKE39 - E39 525i/528i/530i Conforti Cold Air Intake Kit - E39