There are no controls either in InDesign or in Acrobat Pro to change the volume associated with a video file.
I've made many interactive PDF files from InDesign and the volume playing from the PDF is always exactly the same as when I previewed it in the Media panel in InDesign.
Open up the Media panel in InDesign (Window > Interactive > Media) and preview the video there. I'd bet that it previews the same as when you play the PDF file.
There must be something that was done in QuickTime to change the audio.
By the way, you might try converting the video formats with Adobe Media Encoder. It has some nice presets in InDesign CS5.5 and 6. AME is installed with InDesign and the Creative Suite.