Chosen Solution
While cleaning the speaker area I think I may have damaged the screen covering the speaker compromising the water resistance. If I were to seal the port where the speaker is, and I think the mic is right next to it, would the mic and speaker still work or would the silicone create a barrier that sound will not go through?
the silicon will definitely have a negative effect. If they DO still work it will be extremely muffled and no one will be able to understand what you say. I would recommend against sealing the ports for those. Renders them basically useless.