they won't clear on their own, infact they will be even with the rest of the scales. but no worries, drilling them out is very easy. it doesn't pose a problem at all.
yes you can reuse the measuring glass. just wipe it out with some paper towels.
don't forget to check the edges of the scales. its easy to miss a little bit of an edge, might have to use a finger to spread it over the edge if it didn't cover it during pour.
~J