I noticed that when importing a stroke from illustrator to AE to use with stroke effect that when using a stroke created with the brush tool or if I use the pencil tool but I edit the width at one end etc that AE sees the stroke as closed path. Is there a way to import a open pathed stroke which has been either created with the brush or has its width values edited?
No. That's just how it works in Illustrator. Nothing at all to do with AE.