first, SEPARATE THESE BITCHES NOW.
So far you have not had a serious injury, but IMO it is not far away if you do not separate NOW.
My experience with working breeds indicates that spaying CAN help in some situations. My 2 older girls, who now get along very well, did NOT before they were both spayed. Now they co exist very well together. They are also quite a bit older than when they had their altercation. However, with these 2 I never did see any of the growling, up on tippy toe, hard eye contact, etc. There were 2 incidents where the younger girl ripped the older gal's ear. I kept them separated for some time, then once both had been spayed they were pretty easy to get together again.
The growling/threatening from inside the crate is not good news. My 2 girls who hate each other now do this. They SERIOUSLY hate each other, after living harmoniously for almost 4 years together. It is possible as Penny ages, and once she is spayed, that this might dissipate. Time will tell.
However, I will tell you again: Until you get some control on this, your beagle's life is in danger. Your Dobe bitch is capable of killing her in the blink of an eye.
Be smart, and be careful.
I think I advised you to do this earlier, but if you have not already done so, GET PEPPER SPRAY. Keep it in a very handy location, and teach everyone in the house how to use it.
If there is ever a real fight, you will not stop it with your voice. But you CAN stop it with pepper spray, and it might save Emma's life. Don't wait. Separate these dogs, and get pepper spray.
I will also say that this behavior I do not find atypical of a strong temperament working bitch who is becoming an adult. This alone would not prevent me from breeding a bitch.