Honestly I don't think the Zelda MU is terrible for D3. Zelda's advantages in this matchup mostly revolve around her ability to play around Din's fire and cornering Dedede. If she can get a grab, it usually means that you're gonna take 50-60%. Of course, Din's fire is actually kind of difficut to maneuver around, considering Dedede is a giant pear, but it's not entirely impossible to escape. Zelda also likes to counterpick to stages that give her opponents less escapability (like FD, smashville, etc.)
As Dedede, it's very important for you to be able to maneuver around Din's fire. Using waddles to move quickly around the stage is very important. Intercepting Zelda with n-air has been pretty effective for me, even at low percents. Getting grabs is also pretty effective. Zelda is susceptible to downthrow tech chases, and you can get a lot of percent on her if your reactions are on point. KOing her is kind of hard, I will admit, but if you can read where she's going to end up when she uses Faeore's Wind then F-smash is a great KO option. Killing with F-air is also possible, but a lot harder since Faeore's is still really good.
Other moves I've found a little success with are B-air out of sheild if Zelda is hovering around 110% and inhale. Coming down from the air with inhale is not a bad option, and exhaling her offstage can force her to teleport if she's in a bad spot. If she does, you can probably get a downthrow. Upthrow -> Upair also isn't that bad, but I can't tell whether or not it's guaranteed.