Sure small loans have higher rates but they are lower margin and less profitable. They require way more overhead relative to loan size and a drastically higher chance of default (I used to underwrite small biz loans, many times you can’t even get recent and accurate financials - eg for a small plumbing biz). Just look at the market - there’s a reason all the big banks compete to bank Apple but the SBA has to step in to try and stimulate small biz lending.
Those 1000 loans are going to result in millions more interest per year than a single 100M prime loan.