mate there is no way there is going to be anything getting in the flexi hose, it has a very soft metal insert inside it and the braiding gives it strength and obviously the ability to flex.... well thats what i have found on every other exhaust system i have seen, Think about the amount of water that would seap through and then boil in your exhaust pipe when driving downt the road, or how much gasses would escape when you drive down the road.
Blue smoke is usually valve stem seals mate and i know its hard to believe as you have just rebuilt 400 miles ago, sometimes they dont seat right, other brands are shit etc etc.
My advice is to change em anyways if the smoke carrys on going, otherwise youll go round the houses trying to find a fault out because you assumed rather than checked. Im in the middle of fault diagnosis on a fuel issue and i leave no stone unturned as once its done it is done and you can tick it off the list knowing that it wont come back to haunt you. Although things seem pointless and a job lengthener in the short run they dont in the long haul. Hope this helps matey and that blue smoke stops!