I am not sure where this is even turned on. I don't see a setting for this anywhere in my Viasaat equipment or my account settings. Where do you see the option to turn the acceleration on or off?
To answer your question, most web accelerators simply cache pages and images as you browse the internet so that once a particular web asset (text, image, etc) has been downloaded it does not need to be downloaded again. Some others also introduce features to try to block ads, scripts, or other items that may tend to slow down speeds. Turning them off should have no adverse affect other then causing your utilization to go up as now your system may be downloading multiple instances of the same web assets.
Again, without knowing the specifics of where to find what you are trying to turn on or off I can't offer any more information than this.