<< Would silicone caulk do or is there a better item? >>
If all you want to do is keep water from running into the holes, then use
silicone sealant. Keep in mind that from then on nothing else will stick to it.
If you want a little eye candy, see if your local tile outlet has something you
could cement over the hole. if you strike out there, try a stained glass supply
store or hobby store. The stained glass people use small jewels in some of
thier work that can be had in quite a variety of shapes and colors and might be
an interesting variant from a dull old sealant blob. HTH