Those are oil return holes. You can use some RTV to make sure there are no leaks at that mark and you should be fine. Also make sure you get the proper head gasket or at least modify yours so the oil return holes are the proper size. More info..............
Head gasket warning/Oil pan gaskets.
Boiling the block and head make them pretty. I have never done this on all the rebuilds I have done. The Suzuki engine is a pretty tough cookie and I have never found any structural issues with these engines.