Yes it absolutely will show.
The typical test to see if glue will show is wetting it, just as you did.

I tried using a heat gun as previously suggested and it did an amazing job of making the glue disappear, but it takes quite a bit of heat. You will see it change from a white-ish to clear in front of your eyes.

I also tried colored fillers on another boat. Bought about 6 of them to get a perfect match (almost) but when the epoxy covered it the color match disappeared and I had glaring spots of mismatch under the glass.

I wish I could remove the glue with a narrow file or blade and fill again with wood, but I haven't found the right tool to make a neat job of it.

Good luck