I always thought they were vent holes to allow gases to escape during the building process.
On some older frames, pre cartridge bottom bracket, there used to be a grease nipple point to lubricate the balls & axle. As Touche says, there are deliberate holes for gas expansion during brazing, but they are usually confined to the forks & stays not the main tubes. Beats me what the other one is though.Turned the bike over onto its saddle and bars to do a wheel check.
Noticed a small hole on the bottom bracket frame. There is another one in the Top tube
They are all painted as from the Manufacturer.
Are they drainage holes ?
Many Thanks