pin holes in aluminium boat

They used duct tape in WWII, but you aren't working under battle conditions, lol. I'd get a sheet of aluminium or tin, some very good waterproof adhesive, and glue the sheet of metal to the outside of the boat... Cut it to about a 1 or two inch square using tin snips. Gorrilla glue is really good stuff, if you need a glue suggestion.

I don't have an answer - unless you can use silicone - but you should contact a local boat dealer or sporting goods store, they should have an idea of what will work the best for you. You may be able to get some kind of boat sealant.