aah, the 'ol pin hole conundrum. It's not the "stuff" as much as it is the technique and application of whatever stuff you use.
You have to force all the pin holes to show themselves which is really the biggest challenge for getting rid of them. A lot of the time, what can happen is that you will sand the gel coat really thin where a pin hole is lurking just underneath so that when you come back and sand ANY more, you uncover the lurking pinhole.
Other times, pin holes will fill with sanding dust which prevents any filler from getting in there in the first place.
So what you do is to forget about pin holes althogether until ALL of the primary, major filling and/or reshaping is done. In other words, have the part to where you think it should be ready for primer before addressing pin holes.
Now, get out your trusty air nozzle and crank the pressure up to about 125 pounds or so, and then run the tip of that nozzle over the ENTIRE part (every square inch) right on the surface. Any underneath lurking pin holes will be exposed by the air pressure blasting away any thin gelcoat and at the same time, any dust inside pinholes will get blown out as well.
The next step, or trick, is to squeegee on a thin layer of a good polyester filler (I like Evercoat) on the entire part. PRESS HARD as you squish the filler into any hole. Use the edge of your squeegee, not the flat. What can happen is that the air inside the pin hole can act as a compressive barrier to stop the filler from filling the hole. Hard pressure and using the edge of the squeegee helps to overcome that.
When that coat of filler has dried, just sand enough to smooth up the surface. Avoid sanding any further because you could easily sand down even more gelcoat and start the cycle over again.
That's why if you just cover OVER pinholes without filling them, they will still show up as a bubble on that hot sunny day.
Any air pocket (aka "a pin hole not yet exposed") underneath that doesn't get exposed by the high pressure nozzle is probably deep enough to not cause any problems later. However, any air pocket inside the glass does have the potential of showing up later as a bubble under the paint on a hot sunny day.