You should never puncture a roof unnecessarily. That sounds like the work of an incompetent, or at least someone who just doesn't care about being professional; I hope he knew what he was doing with the rest of the job. The fix he did may hold, but I'd be nervous over the long term. What kind of roof is this? If it's some kind of shingles, I'd slide some flashing in underneath each nail hole (and glue in place if there was any question of it slipping).

Assuming asphalt/fiberglass based shingles, probably he applied a roofing cement - silicone sealants generally don't work well with roofing. When you do a repair or in your case a retrofit, often the shingles are too fragile to pry up to put nails for brackets under a tab. The choice is to risk breaking or tearing a tab clean off or putting a small neat hole through it. When I've done work on my own roof I just went right through the shingle. After, if I could break the shingle seal and carefully hold it up I'd put a dab of roof cement where the hole was and mash it down until the dab filled the hole in the top layer. If I couldn't get the shingle up without breaking it, I'd just very carefully apply the cement directly to the hole with the tip of a nail. Concerned about a black dot - just take a handful of roof granules out of your gutter and dust the area if its still tacky.