I have never done it myself but I've heard that you can actually remove that nipple to clean and re-install.Well after trying with various plumbing snakes I gave in and dropped the car off today at the local Merc specialist (D&B in Winford, who by the way are utterly superb).
Both bottom hoses were completely blocked and they unblocked them from bottom upwards rather than top down like I was attempting.
They only charged me 1 hour's labour too which was an unexpected surprise. They leak tested the car and the only remaining issue is water 'weeping' from the C-Pillar drain in the boot (the nipple bit) where the top flexible hose plugs in.
So as the bottom drains are all clear now and at the weekend I'll get out there with the Hylosil Instant gasket and fingers crossed this issue that's be plaguing my car for a while will be fixed !