I occasionally get glue in a hole or 2, I try to get it as quickly as possible, but don't always succeed. Never had water problems though, other than maybe some humidity swelling. When they need cleaned up, I use a simple hand reamer. It was fairly inexpensive, $20 or so? I use no power tools with it though. I just push it straight down in and give it one turn with a wrench. It scrapes out any glue and takes the fuzz off at the same time.
It has helped quite a bit with the new surface clamps too. They were too tight in many of the holes, but this helped  lot.