Puppies do not begin to develop bladder control until around 6 months old. It's not fully developed until around a year of age. What this means is that your puppy is not physically capable of holding it, no matter how small or large a space you keep her in. Will giving her less space help to her learn to hold it longer? Yes. Dogs naturally do not want to soil their dens, but there comes a point when it is physically impossible and she will relieve herself wherever she is.
Your puppy also sounds very bored. The shredding, playing in her own excrement, etc. are all signs of extreme boredom.
Most people who work 9-5ish have a dog walker or bring their dog to a daycare. Certainly if you're gone 12 hours a day, 5 days a week you should make arrangements for your pup to have access to some stimulation and the outdoors. Also, dogs needs access to food and water during the day. A 9 month old dog should still be eating 2-3 times per day (some adult dogs can do just one feeding, but puppies need more). If you're leaving at 6am and not getting back until 5-6pm, when is your dog eating and drinking? Forcing her into a smaller crate than is appropriate with no access to food, water, stimulation, or breaks to relieve herself is abuse. You don't seem like a person who wants to intentionally hurt their dog, more like someone who doesn't want their house covered in poop and shreds of puppy pads and isn't sure how to get that result.
Here are some action steps for you to take, which (if followed) will result in a positive change in your dogs behavior.
- Make sure the crate you have is appropriately sized, not just the smallest one available. Since you didn't mention breed, a good rule of thumb is that your dog should have room to stand up (with her head up, not bent over) without touching the top of the crate, comfortably turn around, and comfortably lay down.
- Ensure you have as consistent a schedule as possible. Try to feed and walk her around the same times every day (dinner doesn't need to always be 6:03 exactly, more like between 6 and 8).
- Give your pup plenty of exercise before you leave in the morning and after you come home at night. 30-60 minutes (varies by breed) at the park each morning will do amazing things for her temperament and behavior. You're not the only person who leaves early for work, there are loads of people with their dogs at my local park at 5am.
- Start some basic obedience training. Find an experienced trainer and enroll in a group class. Again, regular training will do wonders to alleviate some of the boredom and misbehavior.
- Get a dog walker (at least 2 walks/day) or find a dog daycare. No matter how much exercise you give her or training you do it's cruel to leave a dog alone for 12 hours every day with no access to stimulation or an area to relieve herself.
- If you're going to use a dog walker, continue the crate training. Take away the pen, and instead make sure she has things to occupy herself with in the crate. You can feed her meals in a Kong. Get a few of them, whatever size is appropriate for your pup (they're dishwasher safe, so having a few means you don't have to be constantly washing them). Fill it with layers of kibble and other goodies (I use plain unsweetened greek yogurt, baby food, applesauce, fresh cooked fish, cheese, etc.) and then freeze it overnight. Give it to her in her crate as you walk out the door in the morning. It will keep her occupied for a while (my pup takes at least an hour to get through all the frozen food and she loves it), and will also begin developing a positive association with being alone. Make a second one for lunch and have the dog walker give it to her when they get in from walk #1. You'll need 2 walks per day, since you're gone for so long. Once your pup is a little older you could go down to 1 per day if you want.
Again, lots of exercise. Get a dog walker or enroll in a dog daycare. Best of luck.