Yes, that is the killer. I've drilled a small hole through the pad, and filled it with a wire, soldered it, then ground the surface down so the connector would sit flat, but this is so time consuming, and not really effective. Now I just try to keep all the traces running to such things on the bottom. I did get some eyelets, but they are way too large, and clunky!
I think they use vacuum to draw the conductive material through at the same time it is drilled. It would sure be nice to have, but if I got plated through holes at home, next I'd want solder mask...
How do you guys register your double sided boards? I have been etching one side, then drilling a few holes, and using a wire poked through the holes, into the top layer paper, before I iron it to the copper. It works, but it's slow, as you have to etch twice.