That's a good question Michael and one I was always concerned about when I did that mod. Anyway, a few months back my bike got well and truely tested in this way when me and a mate had to ride for several hours through torrential rain. I can safely say that it made no difference to my bike's performance and I had no stalling issues at all.
When I got home though I did check the filter and it looked a bit messy as one would expect so I guess as long as you make sure that when the filter is housed, it sits nice and firm so as not to let any seapage in, you should be fine. That's my experience anyway.
