I think the term you're looking for is underrated, not hated. I do agree that DK gets a pretty crappy representation in Smash 4 (while other franchises like Fire Emblem & Kid Icarus get better treatment despite not being as popular as something like Pokemon or Zelda), but the series is by no means hated by Nintendo.
I mean, it's not like DK got a new game for the Wii U back in February that did really well or anything. If Nintendo left DK to rot in the basement for several years without new games or any appearances in Smash, then it'll be hated by them.