The boats don't have to be found to know that they were there. Flores Island has 800,000 year old artifacts, and during that interval there's never been a land link to the mainland.
Regardless, the oldest craft currently known is the 10,000 year old Pesse canoe.
I should have specified sea worthy water craft that could have carried food, tools, and other life necessities.
Re: Flores Island has 800,000 year old artifacts
The earliest known humans in Africa date from 200,000 years ago, so Flores Island must have a WAY bigger mystery than what happened to the missing boat.