Does setting the "Top" options to zero prevent the parsing and storage of the data or does it just control the display of the tables?

ie. set some of these to zero
#TopSites 30
#TopKSites 10
#TopURLs 30
#TopKURLs 10
#TopReferrers 30
#TopAgents 15
#TopCountries 30
#TopEntry 10
#TopExit 10
#TopSearch 20
#TopUsers 20

Top keywords are just for display purposes and setting them to zero will suppress all reports. The database will still contain all data and can be used to generate a new set of reports later. Note, though, that I haven't moved all filtering to the reporting engine yet, so if you have any hide filters, they will not be reapplied when the report is generated.

If you are trying to avoid report generation, you might be better off using the --batch command line.