Yes, in my opinion its never a problem cleaning up any and all parts of a filter mechanism, including the lip where the water flows over etc. Say you had biowheels or some biomedia like that, you'd just float them in a bucket of tank water which you had just reserved during a water change while you were doing the filter box cleaning, or even just let them float in the tank. People think that sounds yukky but it just pulls the bacteria right back into the filter where it belongs in the hours after you start the cleaned filter back up.
Yes, easy to get fooled by a stray bit of clean silicon and think its a glass crack, I've done that before! And count yourself lucky that it wasn't a real crack. We have a PetSmart tank and matching stand too for my son's tank and during my first setup and fishless cycle, some drops of water got into the hole in the wood where a metal support column was attached by a bolt. The wood was/is particle board and unbeknownst to me, it swelled up, creating a small bump under the edge of the tank. The tank bottom cracked and one night began dumping the entire 28 gallons of water into my son's room. We did get a new tank and stand from PetSmart but the whole thing was a real learning experience and now I pay a lot of attention to the leveling of the tank and the protection of any wood(I have plastic separating the tank from the wood), and I'm careful about where water drops go when doing water changes.
~~waterdrop~~
