Welcome to the forums Bbeachspood,
I dont think bunk beds would be comfortable for a 13 year old that is adult size. But I dont know exactly how large they are.
These two properites are a little different from each other. Both are well rated. Hojos is a more standard Hotel with limited services, but is about an 11 min walk to the Turnstiles that go into Disneyland. You should be aware that the kids suites are extremely popular, but they are all located facing the freeway side of the Hotel, although there are large noise breakers, and would likely not be an issue with the windows closed from reviews.
There are also not that many kids suites , so you may want to check your dates to see if they would even be available which may make up your mind for you.
The Hyatt is very well rated, but as you mentioned you would need to take shuttle service.
There are a variety of other options you could likely choose from, that would be in walking distance to Disneyland of about 15 min with Shuttle service.
If you would like help finding somewhere to stay, you can give a budget per night for a Hotel, as well as what kind of rooms you are looking for ( how many beds ect), and its helpful to include your dates you will be in Anaheim as rates vary widely with the seasons.
You could also consider something that would have larger suites in walking distance to Disneyland....
The Fairifeld Inn.... which is also a limited service Hotel, ( but with mostly exterior corridors) and about an 8 min walk.
Or the Residence Inn Maingate a well rated Hotel about a 15 min walk to the Turnstiles that go into either Park, with Art shuttle service, and full free breakfast, and some weeknight light suppers. Also full kitchens.
Here is a Map of Hotels in the Disneyland area so you can see where things are located. The Disneyland Main Entrance is off of harbor blvd near where it says "East Shuttle Area" on the Map.