I'm pretty sure the only stuff available in the Water Tower after it's destroyed is the Lore that was inside it while it was whole, to make sure you can't permanently miss any. The fake floor you found probably lead to one of those spots.
And as for the key-gun-passable-blockade... derp. This is what happens when you keep adding new areas at random places in the old areas, I guess :P
Knowing me, the reason the blockade is Keygun-based is because the upgrade station in that dungeon is for the Keygun, to ensure you have it in order to enter. And if that's the case, it being unescapable is unintentional.
The missing 5% is a secret area, a secret final boss and an ending tied to that, btw.
As for the stuff that actually is finished: every gun has a secret upgrade, some has two (one gun has two tiers of upgrades, another has two alternate upgrade paths, and another has two complimentary upgrades that can be obtained in any order). There used to be a secret developers' level hidden at one place, I'm not sure it's still accessible and it had some of the most frustrating level design I've ever made so it's probably for the better if it isn't :P And to make things even more confusing, there's a bunch of "fake" areas you can see but aren't meant to access, just to explain how everyone else gets around. (I had plans to let you play as other characters later to let you see the story unfold from a different perspective, but ended up scrapping the idea because it was too much work. The sequence where you play as Emily and all cutscenes you see from someone else's perspective than Mario's are remnants from this)