In the threatrical version Ripley somehow does not drown in her damaged cryotube whilst Newt does, whereas our protagonist in the Special Edition gets washed out on to the beach.
So in the theatrical version there would have had to be an air pocket in which Ripley survived and so did the Facehugger, later on, we even see the Facehugger crawl down from the enclosed end of the EEV away from the water.
In the Special Edition judging by Ripley being washed out everything not impaled by safety support or securely drowned would have been flushed out, including the Facehugger that in this scenario would have to learn how to swim, and fast.