It's probably not so much about Nintendo specifically as one advertising partner, as much as it is about encouraging the advertiser ecosystem to be comfortable

It's probably not so much about Nintendo specifically as one advertising partner, as much as it is about encouraging the advertiser ecosystem to be comfortable with continually spending money on Youtube as a platform. If Youtube removes dislikes, there is less risk for these viral "dislike" moments to happen, which can make content producers and advertisers nervous. Additionally, Google probably puts way more resources than you might expect into things like moderating the usage of the dislike button and making sure it isn't exploited by bots, nefarious actors, etc. Not much downside from the business side of Youtube in taking steps to sunset the button.