Hi,
If you want to have the sign smaller, you can always edit the currency symbol via the menu System->Currencies and add a span and some styling like that:
<span style="font-size:10px">€</span>
However, for the price pieces themselves, there is no option to change their size. You will have to hack in the numberFormat function of the file administrator/components/com_hikashop/classes/currency.php (beware that it's complex code there).
On the Display tab of the configuration, if you select "inherit" it takes the default layout. So that's basically the same.