The way you would loop through them is to first get a reference to the nested Repeater:
Repeater rptInterests = (Repeater)rptInterestCategory.FindControl("rptInterests");
And then you can loop through the data items, find the checkbox, and get the value of the CheckBox:
foreach (RepeaterItem item in rptInterests.Items)
{
CheckBox cbInterest = (CheckBox)item.FindControl("cbInterest");
bool isChecked = cbInterest.Checked;
}