My immersion tells me that when I come across one of those skimmer sites, it is some other mission that I'm not personally on. It makes sense for them to be out there (randomly) if there are some times when it does matter. I totally agree that the canisters are very rarely economically viable to pick up.
As for the materials, are you dropping into Points of Interest (blue circle on the planet radar seen at ~2-3km altitude)? Points of interest are supposed to be hotspots for more random surface encounters (including materials).
I visited a planet with a Detailed Surface Scanner and had a field day finding a lot (when I landed, three good outcrops were within sensor range of the SRV and plenty more were nearby) of good materials in one of the Geological Features that showed up after probing the planet. The others on the same planet weren't as good as the first, though, so there appears to be some variety in those as well.
As for the bounty, I'd check with an Interstellar Factor as the fine/bounty you gained would have been with the faction that operates the skimmers and if that faction wasn't present in the station you stopped in, it may not show up. With the new-ish C&P mechanics, if it's a bounty, you might have to visit an Interstellar Factor to pay it anyway.