Honestly? I don't think it matters until you get to a certain size (and I can't, for the life of me, remember that size...). The thing is to find a method and then stick with it, hopefully it'll be in such a way that you never need to touch it again. My own advice, without anything as convincing as evidence to support it, is something akin to your own suggestion:
c:\<customer_id>\<document_year>\<document_month>\<document_day>\actual_file.tif
I'd also raise the suggestion that, depending on your server setup, it might be worth giving each customer (depending on the amount of data or account type) their own drive/partition.
Bear in mind that, without some sort of user-control or permissions system, that file-paths could be predictably guessed and browsed (as if you didn't know this already...I know, I'm sorry). The fact that you raised the bullet point of 'six digit unique code' suggests that you don't need a path of common-format, but I would suggest that a common-format (of whatever format you end up choosing) would be a better idea.
Back in my Windows days I sorted my own directories around the file's primary-relation, it'd be considered a 'tag' nowadays (c:\documents and settings\university\year1\module21\assignment1.doc
for example), this made it easier to find things later. Your customers appear to have their directory structure enforced -by you- but finding things that they did last week is easier if they only have to traverse the date, remembering where they put something last week when they get to the six-digit unique number-named folders is going to be, well, difficult. At best.