Kind of vague statements. Also, numbers are very ambigious. What's 55-45 for some is 60-40 for others. What's 60-40 for some is 65-35 for others. Etc etc.
I'm going to try to deter from ambiguities as much as possible and actually discuss why I think the match-up is never more than slightly in MKs favour. I'm also mainly going to talk about Bananas, since that's what we've been focusing on. I don't really know where to start...so sorry x.x
Let's just get this out of the way: you really shouldn't worry that much about MK getting your bananas, at least not as much as you would against Marth. If MK DOES, by any chance, get your bananas, know that he has an absurdly long glide-toss. This is good and bad for you, good meaning that it's really predictable when he wants to approach, but bad because if you aren't paying attention and sheilding or spotdodging, you get a GT to Dsmash in the face. That's not fun.
Generally, people with longer glide-tosses are more predictable with their approaches if they have an item, although they can get in your face if you don't take the right course of action. Granted I don't play the good MKs that Player 1, ADHD, and AZ have played, but baiting a GT->Dsmash has been relatively easy. You can sheild the Dsmash and then grab. Immediately going after your banana could mean you get shuttle looped or aerial'd.
Next point, when bananas are in your control. When you glide-toss a banana towards the MK, they can either sit there and take it (good for you) sheild it (common, meh for you) or spotdodge it (neutral, unless you're really close). If they sheild it, against a lot of other characters, you can just shorthop and z-catch it and follow up with a dthrow that could hit them or that could land on the ground and be yours to waveland throw (instant aerial GT or whatever it's called, I forget x.x). However, if you're being predictable with this, the MK could just shuttle loop or fair or uair and get you.
Technically, you could do the aerial dodge catch and have him whiff his shuttle loop, but if he tornados then yeah. Basically, it's best to go for the grab if he shields, otherwise he has too many options.
It's been pretty accepted that fighting MK as Diddy offstage is really not fun. Nor is it that fun in the air. Not so much that flat ground (FD) is the best for your playstyle, but you probably don't want to play MK on Rainbow Cruise. You need some solid, main platform. Because his offstage game is crazy. If you're trying to Rocket-barrel to the ledge, chances are you're going to get gimped. When recovering, I try to charge the barrels away from the ledge and curve over the platform (at low percents). At high percents where MK could punish that with a killer dsmash or something...I don't really know what I do, x.x. Play as far away from the ledge as possible and don't attempt chasing him offstage. You can still do things like space Fairs to hit him when he's being cornered to the ledge, but just don't get close to that ledge yourself.
Some MKs Dair camp. Well really like all of the ones I've played do that, but I don't play great MKs like I said, so I'm not sure if the great ones do that. However, if your opponent does Dair camp, he's probably trying to bait a banana throw by getting close to the ground and just doing another mid-air jump. You can always just short hop throw, or dribble away, or get under him, sheild, and throw up, or whatever.
In this match-up, you want to be assertive but not offensive. During ADHD vs. M2K in the Get gimped Grand Finals, M2K was being in ADHDs face a lot, but ADHD snuck in attacks while staying on his toes, dribbling bananas and being ready for his opponents openings. Sorry if that wasn't such a fair statement to the game, but that's how I took it, and it's helped me a lot in the match-up.
When you get an opening, like when your bananas hits his sheild and you're close enough, or you make him trip or whatever, go for it and follow it up. However, "Don't jump into the ****." Don't do stupid things like jumping offstage and attempting to Dair spike the MK. After a point where the tides could turn, get back your banana control and start dribbling and such to keep the bananas in your control. If you want to think in terms of zones (yay HugS) you want to always be in either a positive or neutral zone. After you get your quick grab->banana throw->fair or whatever, control your bananas again.
...I basically rambled about arbitrary points in the match-up. But it's definitely not worse than 60-40. Diddy has the tools to get past Tornados, Planking, Dair camping, and quite a bit of what Meta-Knight has. He can assert neutral positions with his bananas. The match-up, in my opinion, is pretty even.
Edit:
One of my favorite things to do, is to merely z-catch an item and then z drop it immediately, wasting almost 0 time, and maintaining access to my entire moveset while disabling the hitbox of said thrown item (I generally call this tactic "defusing")
If a MK could reliably defuse bananas, then wouldn't Diddy lose an extremely powerful tool?
Don't forget that Diddy can diffuse back.
And the chances for MK being able to do this, against a Diddy that can control his bananas, is quite rare. If a banana hits an MKs sheild, the Diddy can either just grab or fair grab it before MK can (before the sheildstun).
Assuming that he can, however, then he kind of does? The situation remains somewhat neutral until action is actually taken. However, if the MK decides to pick up the bananas, his approaches are generally obvious (long GTs aren't that great), and Diddy can pseudo-camp with peanuts if MK decides to just grab the banana and run around his side of the stage.
In my head (I don't have MK match-up experience against great people, and the bit of times my bananas do get diffused, the MKs do a predictable glide toss approach) the best thing for the MK to do in that situation is leave the banana on that side of the stage and do one of his original approaches, assuming Diddy doesn't have a second banana. This would catch the Diddy off-guard, and if he tries to get his banana back the MK can punish.
That's just a mental thought though, and I'm not sure how well it would translate into an actual game.
It's just that...that idea you mentioned doesn't work because MK has to get the chance to diffuse in the first place, and that's if the Diddy doesn't already have a second banana in his hand (which most of the time, he should).