The water drains out of the tubes plenty fast anyway, since they are completely open on the ends... Wheeled a LOT in college and we all had solid axle rigs. None of us had issues with river crossings or the like, only when submerged for significant time at fairly impressive depth did we get water in axles... If you are getting water in the axle during fairly quick crossings, you might re-check the seals. If the seals are that bad, I would think you would also have issues with oil coming out, but that might take a while to show if you just replaced the seals... In my experience it is fairly easy to cut the inner seal of the long shaft when you install the shaft. Also had a friend install the seal backwards, and then roll off the spring when he pushed the shaft in. Sucks to change it out again, but might be something to watch for. If oil leaks out that side, you probably nicked the seal putting the shaft in...
I would NOT drill a hole in the axle tube. You are just letting water in to the seal area faster, and if the seals are bad for whatever reason, you'll have just as much water in the axle, and a hole that you don't need weakening the axle tube...
Good luck!