Old drill holes under toilet

Hi I hope this question doesn't sound too silly

Thing is I bought and installed a new toilet few months ago. Naturally I had to drill new screw holes into the floor to fasten it. I didn't do anything with the old holes, I just placed the toiled over it since the holes weren't visible under there. I noticed that the toilet doesn't completely touch the floor in the front, whether this is because the floor is uneven or the base of the toilet I don't know, I didn't really mind since the toilet sits stable.

Since then the floor around the toilet has gotten wet after shower (the toilet is beside the bathtub) and from condensation of the toilet tank (the tank gets a lot of condensation, don't know why). I am worried that water has escaped into the old drill holes under the toilet and if that is something I have to be worried about since it is a concrete floor it could crack. I am planning to chaulk the rim of the toilet base because of this (there is a space between the floor and the base of the toilet because of this unevenness).

Do you think I have to remove the toilet and check for water and moisture before I seal the base of the toilet with silicon chaulk?

Old drill holes under toilet