Sure it would be nice to have them in folders but then if they are in different database you have to manage those database as well, synchronised backup for one. But hey, I never used a product with many databases so maybe it's not that bad idea, I just told you want I've seen.

One of the apps I'm talking about has around 400 tables. The two first letters of the table name indicate the module to which the table belong:

APxxxxx = Accounts Payable Module
ARxxxxx = Accounts Receivable

COxxxxx = Company Wide (not much talbes but a few ones)

It's not hard to find a table using this approach.

HTH