The reason was obvious. Both Donkey Kong and Master Hand are still considered villains in at least some more recent games. The others characters might of had an excuse for removal, but Donkey Kong is the main antagonist in the Mario vs Donkey Kong series and Master Hand continues to oppose and manipulate other characters with his forces in the Super Smash Bros. series.
If it bothers you I didn’t leave a reason, then I apologise and I’ll try to leave one in the future if I revert your edits.
It's okay, I do see your points. Though I removed Master Hand from playable characters section because, sure, he was legitimately playable in World of Light, but other than that, he's only ever playable via unofficial means and he isn't part of the main playable cast. Plus, he's already grouped in with the bosses, which he fits in under much better.