Mapping Subdomains on a SubDir network

Ok, I know this is a well kicked horse in the WPMS world. But my company is working on a network and we have to make the decision to go Subdomain or SubDir.

The client would like to use SubDir for aesthetic reasons (the site will sell prepackaged sites using Pro Sites).

I have no problem with this, but I have a few concerns I would like to run by the community.

First, aesthetics aside is there any technical reasons a subdir site is going to make my life or the clients life harder once they have 1000+ sites in the network?

Second, I worry about the brand growing and the desire to have true sub domains that share WP user data. For example:

mysite.com/yoursite/ is fine for now. 'yoursite' is the product.

As the brand of mysite.com grows, the client may come back to me and say ... "I want to open a storefront at store.mysite.com and it has to share all the user data and have a common toolbar with all of the network sites"

When they tell me this (and I am betting they will) I want to make sure I have not backed us into a corner.

How do you have a subdir install while still maintaining the ability to add subdomains that share the network?
Do you install subdir and use Domain Mapping to add the subdomains later?
Do you use the Multi Network Plugin?
Is there some other best practice that folks are using to make this happen (I am sure I am not the first person to have this dilemma)?

As always thanks for your time and support in advance!