Attacks on civilians were not as common as they were in say, Europe.

This partly has to do with the largely shared culture, ethnicity, and language within the internal combat of much of Japan's history.

There wasn't a real concept of being 'Japanese' outside of "we are more similar than we are different compared to someone from China, Korea, Portugal, etc". But the similarities meant that it was harder to perpetrate atrocities on civilians and easily pass it off as not hurting 'people'. Attacking villages, towns, ports, and traders would hurt your commerce as well since they were heavily associated.

Compare this to Iberian Christians attacking Moorish villagers.

That being said, sackings, rape, and pillaging did still occur in wartime Japan.

Another reason why civilians were often not attacked in Japan was because much of warfare was one of conquest in the sense that if they defeated their enemies, they would simply take their place in the current framework. Not much would change in the daily lives of most people.

And of course, the tradition was to surrender and join the winning side if one could not win. This was a standard in Japanese warfare. This further reduced the need for destructive tactics to starve or destroy the tax base of an enemy by pillaging and targeting civilians.

There was often no incentive to wipe out large swaths of the civilian population. It would be counter productive to burn the farmlands that you planned to own. That being said, particularly bloody feuds between clans/lords did sometimes lead to reprisal attacks that were meant to wipe out the other side, including civilians.

As for a honor code, there were various civilities, mannerisms, and rituals that warriors were supposed to observe. But they were not 'honorable' in the way that we would use the word.

These codes were not about compassion or helping the weak. They were a set of guidelines on how to be a loyal vassal, the duties of a warrior to his lord, and the manners of their station in society as professional warriors.

These customs changed a great deal depending on what time period we're talking about, as well as regions. There certainly was no 'universally' recognized code of honor that everyone adhered to, or even claimed to adhere to.

And even these customs were often broken if it meant getting an upper hand in a fight.

No one would consider threatening to execute children hostages honorable, but it was certainly done by samurai. The idea that a samurai would never use 'dirty' methods to win fights is laughable. Betrayal happened so often, you could easily substitute Japan for Westeros.

As with any other autocratic rulers, there were some benevolent despots and there were some power abusing rulers. At the end of the day, the higher class had privileges and rights that were denied to the common people, and most would not hesitate to disavow commoners of their rights if they thought it was in their best interests.

The various philosophies around proper rulership over the people generally revolved around Confucian and later Neo-Confucian ideas. These extolled the idea of a benevolent king/emperor and emphasized his responsibility to the people as well as the need for the people to be subservient to their ruler.

All of this isn't to say that Japanese rulers were all heartless monsters, simply that they were not particularly any nicer than other rulers anywhere else. There were good rulers who cared about the people, there were bad rulers who exploited the people, and all of them were human, like any rulers anywhere.