Does the loan hurt you on poptropica Skullduggery Island?

No, they do not.

Most players will not repay their last loan, which can be up to 500,000 doubloons to buy a Phoenix Warbird. Since the only penalty for not repaying an overdue loan is that you cannot buy a larger ship, you would not be affected at all.

You should always pay back a loan as soon as you can because you pay 5%interest for every "day" up to 20 days. However, since a "day" only passes when you leave one island and arrive at a different one, you can limit the number of days that pass as well (leave an island, collect salvage, and go back).