There aren't any utilities for querying data, yet.
At the moment, the plugin intercepts calls made to ACF's get_field(), the_field(), update_field() etc functions and plugs data in from the custom tables. So, it's a seamless API when using ACF in a template context.
The benefit of having the data structured is that you can use WordPress' $wpdb instance to query the data in any way you need — this is where the real performance gains come into it, especially when searching/filtering across many different fields.
I have a simple example of using custom table data in conjunction with WP_Query here:
There are also a number of filters within WP_Query that allow adding clauses such as JOIN and WHERE clauses. I don't have a polished example of how to use these just yet but I do have a Gist you might like to have a peek at:
If custom SQL is new to you, you might also want to start with the primer I wrote for SQL & WordPress:
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