HeeHee.....I have 3 holes in my bladder 2 are intake and one is outgoing and I haven't had any trouble with my dives even with all those holes. You are luck that yours are only pin holes.
The super glue (CyanocryAnylate, CA) should be good if you allow it to set up over night, But CA is a brittle glue and if the bladder moves alot the glue might crack and fall off and/or contaminate your bladder with small pieces of glue.
Shoe goo is a much more flexable type of glue and would work much better. You will want to test the glue you might use in an area that won't effect the bladder if things go wrong between the glue and the plastic in the bladder material. Super Glue doesn't react well with some plastics like Poly-foams (beer cooler material) It eats the material up. So if your bladder reacts poorly to Super Glue your pin hole will end up being a Big hole.

This is a repair that YOU can do but if you aren't comfortable with it your LDS can handle it too.
......OR you can just keep adding air to your bladder!