Electrical engineer here. I can only answer a few of the questions:
This will be a "USB Device" (as opposed to USB Host or USB OTG) so the correct USB connector to use is B receptacle, mini-B receptacle (obsolete), micro-B receptacle (obsolete), or C receptacle. You can pick any one of those. The obsolete ones still work fine, it's just hard to find cables for them. Mini-B is actually very durable. Alternately, you could have a captive cable with a USB A male plug on the end.
KiCad has pretty good facilities for making your own component layouts. Many components you simply can't find existing files for. Unfortunately, this is part of the life of circuit design. It should only take an hour or so per component.
Adding diodes can enable N-key rollover. If you don't need that feature, you could skip it. If you're going to the trouble of making your own keyboard, diodes are a comparatively small cost, so you should do it. The Chouchou keyboard uses a separate pin for every single key, so it doesn't need diodes.
Yes, you can hide the parts in a case. But you could also just make the back of the circuit board really long, and there should be enough space for it. Picking out connectors and cables and stuff is always a pain, so try to avoid having multiple boxes if you can. The electronics should be pretty small anyway.