So when I am gone for the day I leave my 1.5 year old GSD in her kennel.  Right now she can't be trusted out of it by herself.  Anyway, it doesn't matter how long or short I am gone she always shits in her cage.  I can take her outside right before I leave and there have been times I was only gone for 30-45 minutes and she has shit in the cage.  To make matters worse she usually lays in it.  She has always done this, whether I give her very little room to move around, put a bed in, she will still shit all over the bed and lay in it.  Is there anyway at all I can get her to stop doing this?  Will it go away over time maybe?

Tough call. Maybe it will go away. Yet I had a dachshund that was so stubborn she did it just for the hell of it. Sounds like you might have a GSD just as stubborn as a dachshund which is one of the most stubborn dogs around. Yet don't don't piss them off cause there were bred to go into badger holes.

Set up a wireless camera to see how quickly she goes?  Maybe that's her reaction to separation anxiety?

My latest puppy Akita (now 3.5 years old) didn't poop, but he did pee and lay in it in his crate. This is unusual for an Akita because they are typically very clean.

My initial response was to scold, take him out for a pee, which didn't always work, then clean and put him back in.

This had zero effect on the behavior, even when I made his crate the size of a shoe box. He would happily lay in his own pee.

Eventually I interpreted this behavior as a call for attention and an opportunity to get out of the crate.

My response was to give him absolutely no attention at all. No scolding, no emotion, and as little out of the crate time as possible. I would tether him to the crate with 12" of lead, clean the crate, clean him, and dump him right back in. Absolutely no talking, not even to my wife. As minimal event as I could make it. No attention at all. That fixed it.

Can't say that your dog is in the same category, but just throwing this out as a data point.