I have the Moko Slim-Fit Multi-angle Folio Cover Case and it has a cut out area so you can attach the pogo connector with the case closed. If you really want to have it connected while in a standing position, you might consider getting a tablet stand like this one that leaves room for the connector. You might have to leave it hanging over the edge of your shelf or desk, but it would work.

But, no, I do not believe there are any 90° pogo cables and even if there were, I doubt they'd be flush enough to fit in your case.

I just got http://www.amazon.com/gp/product/B00A9G985S/ref=oh_details_o00_s00_i01?ie=UTF8&psc=1 I haven't had the chance to try it out, but it looks pretty nice

Bought this one a few weeks ago and am really happy with it.

http://www.amazon.com/gp/product/B00A9G985S/ref=oh_details_o01_s00_i00?ie=UTF8&psc=1