"The image of a comic book character, ie the style of the face..."
Both. The original artwork is protected by copyright law, and its use in trade is protected by trademark law. So, someone who produces a derivative work and uses it in trade should expect to be sued under both bodies of law.
"Assuming that they fall under trademark law and the entity which holds the trademark is a Japanese publisher, who would have the standing to pursue a trademark infringement case against..."
International distribution agreements often have clauses where one company or the other is authorized and given the duty to sue for rights infringements in country. Without knowing what those agreements say, it's tough to tell, but the default would usually be the original rights holder.
"In the event of such a case, what impact would a decades long practice of tolerance for fan art have on the court case?"
On a strict trademark case, the past permissiveness could possibly show that the company has abandoned rights to the mark or allowed it to become generic. The analysis under copyright would probably be different, and center on estoppel or laches.
"I see a distinction drawn occasionally in copyright and trademark articles regarding the concept of something being produced "commercially". What does this term mean in context?..."
The commercial or non-commercial character of the use can be important in an analysis of fair use. In a fair use case, a work being produced for commercial use typically works against a finding of fair use, and thus works against the defendant. Often, in a copyright fair use case, one of the bottom lines for the analysis is market displacement, which measures the amount of the rights holder's market that the alleged fair use usurps. I would guess that the fact that these artworks are being sold at auction would not militate to the favor of the defendants.
In a trademark case, there is typically only infringement if a mark is unlawfully used in commerce. So, if someone was making fan art for their own use and not distributing it or displaying it in any way, the likelihood that there would be trademark infringement would be very low. Again, though, a sale at an auction is pretty commercial.
"If the trademark holders have shown zero interest for decades in making any effort to stop the sale of fan produced artwork, is there really any need for convention organizers to be concerned about suddenly being sued out of existence. Isn't it more likely that trademark holders would send a cease and desist letter before any legal action was threatened?"
Possibly, but a cease and desist letter is not at all required before a convention organizer is sued out of existence. Some attorneys take the stance that cease and desist letters just give the defendant more time to circle the wagons, and that a summons delivered out of the blue can be a more effective way to deter an infringing use. Again, laches could potentially be a defense, but it'd need to be proven in court, and most con organizers I've known are on shoestring budgets that wouldn't really support them fronting the kind of money a defense like this would cost.