Numinix has a "Extra Product Fields" addon that will add a ISBN field to the database. Not sure if it creates an additional TABLE, or whether it writes the field to the PRODUCTS table. If it does the latter, you can reconfigure Easy Populate to include that field, and thereby make it possible to load all 100,000 books using EP.
If it does NOT write the field to the PRODUCTS table, then EP may not be suitable - you could then look at APSONA SHOPADMIN instead.
If you wany to use CORE zencart (no additional fields) you can write the ISBN to the MODEL NUMBER field, and could probably rename the defines for "Model" to say "ISBN" instead.
However... if you later wish to use Google Merchant Center, you will need to reference an ISBN field - and Numinix's addon will give this to you. When used with Numinix's Google Merchant Center module, you will be able to generate XML feeds that meet Google's requirements.