I would suspect, not the estrogen, but rather an irritation from the trachea tube for a laryngitis cause.
Another possibility is a thyroid issue coming to the forefront with the hormonal change. This can cause laryngeal paralysis in some dogs and can impact ability to eat also.
An upper respiratory infection can cause voice loss too.
If your vet isn't sure what to do then you might want to see a vet who specializes in small animal internal medicine.
http://www.acvim.org/Specialist/Search.aspx
You didn't mention how long this has gone on. If its been more than 10 days of illness and meds not working I'd say the specialist might be a good idea.
Hope this helps you!
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