[texan]

It's called hydrolock, and will only happen if the filter is submerged underwater and the engine is running (and running above idle). If significant amounts of water enter the combustion chamber, when the piston comes to TDC and tries to compress the uncompressible fluid something will break. Hydrolock is a very rare occurance, but if you are truly worried about it just do what the factories do, place the filter in an airbox underhood and run a pipe from there to outside the engine bay.