While a hydrophillic coating might sound good in principal, I think that you will find a couple of issues in practice. What you are hoping for is something to spread the water into an optically flat surface over your filter. While that might work if the filter is horizontal, a vertically mounted filter will tend to smear in a downwards direction as gravity pulls on the water. This gets worse as the amount of water increases. And regardless of orientation, any small bit of dust or dirt will tend to create a lens effect much bigger than the size of the dirt, such that small particles that would not be noticable dry become much more visible on a hydrophillic surface.
I would probably agree with you until I saw this video from
Petapixel.
Wikipedia page about this subject (interesting!)Hot glue and silicone sealant.. need I say more? 
One other tip. for small holes, try melting them carefully with a soldering iron, rather than drilling them, this works particularly well with brittle plastic, (and strangely also with bamboo, which is also difficult to drill, but that's a story for another day) so long as you don't mind the smell. Do this in a well ventilated area, some plastics will produce cyanide laden fumes... not too pleasant.
I managed quite nicely. I agree that silicone sealant is great, I used lots of it around the lens filter. But on the connection to the tripod I used steel screws, so I felt like sealant wouldn't work that well there. I ended up using rubber O-rings and some fiber gaskets, works great! I'll make some detailed photos when I get the change.
Perhaps I'll even make a V2 box and take photos of the building process.
Drilling holes is no problem. I've not attempted any cuts with a knife anymore however ;-)
Last year, I completed a nine month time-lapse of an apple tree.
The camera box was at ground level, pointing upwards at 45 degrees towards the sky.
I built a 600mm deep open-ended enclosure around and in front of the box.
Despite really bad weather, there was rarely any rain drops on the plain glass filter fitted to the box.
David
Would you have any photos of the rig? I need the widest angle I can get, so I can't obstruct the lens too much.
