The first argument of theme_table ($header) consists of a structured array for each column header.
The 'sort' value supposedly allows to set a default sort order for this column. This would be very convenient - simply set this to 'desc', and from now on, a click on that header will first sort the entries in descending order. This saves an extra page load in fields that are routinely sorted in descending order.
However, instead of actually changing the default sorting direction for that field, it seems to set the current sort order to that field and that direction - as indicated by the little triangle next to the column header.
If this is intentional, the API page should probably be rewritten to make this clear. In that case, this is just a feature request for a default sorting order as described above.