Yes, After Effects CS5 does make use of hyperthreading. If After Effects isn't using more than a certain number of processors, it's because you have your Memory & Multiprocessing preferences set to reserve some threads for other applications and/or because you don't have enough RAM to feed more processors.
48GB is enough for 12 processes at the recommended 4GB of installed RAM per processor that will be used for After Effects rendering.
See
this page for information about memory and performance in After Effects.
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Todd Kopriva, Adobe Systems Incorporated
Technical Support for professional video software
After Effects Help & Support
Premiere Pro Help & Support
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