You did not damage the microphone. Both the holes for both of the mics face downwards for the actual mics themselves. There is one on the I/O board where the USB is, this one is for when you have the phone up to your ear talking on the phone. The mic at the top is located on the board itself and is for the loudspeaker function such as speakerphone. If you want to test to see if the mic works then simply type in your keypad *#0283# and this will take you to an audio test screen, from there click the second one down from the top, it should say something like "SPK mic" or "2nd mic", then just speak into it and if you hear yourself then it works.
As for the water resistance, I highly doubt that you damaged any water water resistance. Both of these mics have the same setup, under the mic holes is a rubber grommet and literally all but flush with the holes with the mics themselves is the water resistant mesh. That being said, both of meshes are parallel with the phone. They aren't where the outside hole is, but in the hole and upwards if that makes sense. Just to make sure it does, when you stuck the SIM ejector in, it went in parallel with the mesh rather than into the mesh. So you're good.