We encountered a similar problem with case folders. What I ended up doing is breaking them into alphanumeric subfolders.

Depending on how you utilize them, you could break them into lettered folders based on the customer name, or numeric folders based on a customer ID number.

For example, you could create subfolders for A-Z and route them based on the first letter of a last name or something along those lines.

Really it depends on how you manage the accounts. A lot of options exist like breaking them into region/city or zip code, then A-Z subfolders, etc. to make each folder have as few as possible.

The "best" option is really going to depend on how your users operate.