I want to do this, but I haven't convinced myself to do it yet. When I do, every hole will be reinforced. I know there are framebuilders that have a policy not to drill holes. Some people drill lots of holes.
Where is the wire going from the hole in the chainstay? That seems like a strange place to get the wire out. This one needs a reinforcement, there is a lot of flexing here.
The small holes are actually vents; they are the vestiges of construction, they probably are a bad thing on a bike in use.
Just as a point of reference, water bottle bosses are 1/4" holes.