I have seen projects in cook with 80 tables, so don't worry too much.
If you think it will be huge, think to developp you application in splitted components. One component for engine, another one for reporting, etc...
Try also to merge your tables for simple lists,
When you have multiple tables with the same columns defined, you can optimize, such as CCK or com_categories. There is a field that specify the context of the data. So the same table can store items for different purposes. In this way you can put many tables in the same one