If you look at the gerber of a soldermask layer, what you’ll find is that it’s actually a negative layer. Soldermask goes everywhere on your PCB except where you have features in that gerber layer. And yes, you need to have holes in the soldermask around every pin and pad that you want electrical connections to, because you can’t make electrical connections through the soldermask.
By default, gEDA puts a hole in the soldermask around every SMT pad in a footprint, which is how it generated the holes in the soldermask above your footprint.
For the next round, you should probably skip the .png portion; you could even modify StippleGen to output your pins and pads, so that you skip inkscape entirely. :)
Also, it’s a *very* good idea to run the DRC (design rule check) on your PCB before even exporting to gerber. It will make sure that you don’t have any features (let alone 20,000) that are too small to fabricate.
